Chimeric pro-caspases and methods of using same

ABSTRACT

The present invention relates to a chimeric pro-caspase, which contains a pro-caspase domain and an oligomerizing domain. The invention also relates to an antibody that reacts specifically with a chimeric pro-caspase. In addition, the invention further relates to a polynucleotide encoding a chimeric pro-caspase, and to nucleotide sequences, which can hybridize specifically with a polynucleotide encoding a chimeric pro-caspase. The present invention also relates to a method of inducing apoptosis in a cell by providing a chimeric pro-caspase in the cell, wherein the chimeric pro-caspase includes a pro-caspase domain and an oligomerizing domain, whereby the chimeric pro-caspase forms an oligomer in the cell, thereby activating caspase activity of the chimeric pro-caspase and inducing apoptosis in the cell. The present invention further relates to a method of reducing the severity of a pathologic condition in a subject, by providing cells of the subject that are involved in the pathologic condition with a chimeric pro-caspase comprising a pro-caspase domain and an oligomerizing domain, whereby the chimeric pro-caspase forms an oligomer in the cells, thereby activating caspase activity of the chimeric pro-caspase, inducing apoptosis in the cells, and reducing the severity of the pathologic condition in the subject.

This application claims the benefit of priority of U.S. provisionalpatent application Ser. No. 60/108,873, filed Nov. 17, 1998, the entirecontents of which is incorporated herein by reference.

This invention was made in part with government support under Grant No.RO1 CA51462 awaraded by the National Institutes of Health. Thegovernment has certain rights in this invention.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates generally to molecular biology andmedicine and more specifically to pro-caspases that have been modifiedto facilitate directed oligomerization, and to methods of using suchmodified pro-caspases for inducing apoptosis in a cell.

2. Background Information

In essentially all self-renewing tissues, a balance is struck betweencell production by mitosis and cell loss due to programmed cell death,thereby maintaining total cell numbers within a physiologicallyappropriate range. In pathological conditions, however, the balance incell production and cell loss can be disrupted. In cancer, for example,an increased amount of cell production due to a shortened cell cycletime or to a decreased amount of cell death can occur due todysregulation of a programmed cell death pathway, resulting in growth ofa tumor. Dysregulation of apoptosis also can occur, for example, inneurodegenerative diseases, in which neurons die prematurely, andinduction of apoptosis can figure prominently in the pathophysiology ofdiseases associated with viral infection.

In multicellular organisms, homeostasis is maintained by balancing therate of cell proliferation against the rate of cell death. Cellproliferation is influenced by numerous growth factors and theexpression of proto-oncogenes, which typically encourage progressionthrough the cell cycle. In contrast, numerous events, including theexpression of tumor suppressor genes, can lead to an arrest of cellularproliferation.

In differentiated cells, a particular form of programmed cell death,apoptosis, is carried out when an internal suicide program is activated.This program can be initiated by a variety of external signals as wellas signals that are generated within the cell, for example, in responseto genetic damage. For many years, the magnitude of apoptotic cell deathwas not appreciated because the dying cells are quickly eliminated byphagocytes, and in the absence of an inflammatory response.

Various diseases, including, for example, cancer, inborn errors ofmetabolism, and neurodegenerative diseases have been refractory totreatment. Recently, however, gene therapy has begun to emerge as aviable means to treat such diseases at the cellular level. Althoughclinical trials of gene therapy protocols have yet to producestatistically significant results, positive results obtained in patientstreated by gene therapy cannot be ignored, particularly since genetherapy generally has been practiced on patients that have failed moreconventional treatment protocols.

Although gene therapy holds great promise to alleviate and cure variousinherited and acquired diseases, it must be proven not only efficient,but also safe, in order to become a routine clinical procedure.Unfortunately, genetically manipulated cells can acquire unwantedproperties and become deleterious to the host due, for example, toinsertion of an introduced gene into an otherwise normal gene in thehost cell, thus disrupting the function of the normal gene. A methodthat ablates such cells can provide a safeguard against unwanteddeleterious effects and, therefore, is highly desired. Ideally, such asystem should effectively and specifically induce apoptosis, aphysiologic form of cell death that rids the body of a cell withouteliciting a harmful inflammatory response.

The mechanisms that mediate apoptosis have been studied intensively, andinvolve the activation of endogenous proteases, the loss ofmitochondrial function, and the appearance of structural changes such asdisruption of the cytoskeleton, cell shrinkage, membrane blebbing, andnuclear condensation due to degradation of DNA. The various signals thattrigger apoptosis are thought to bring about these events by convergingon a common cell death pathway that is regulated by the expression ofgenes that are highly conserved evolutionarily. However, while numerousgenes have been identified as involved in process of apoptosis, themechanisms by which the products of these genes interact to execute theapoptotic program is not well understood.

SUMMARY OF THE INVENTION

The present invention is based on the seminal discovery thatoligomerization is sufficient to initiate pro-caspase processing in vivoand in vitro and to activate their cell death activity. Given thisobservation, the inventors have produced chimeric pro-caspases, whichcontain a pro-caspase domain and an oligomerizing domain. In oneembodiment, the pro-caspase domain is pro-caspase-8 or a peptide portionof pro-caspase-8, which has caspase-8 activity potential. Thepro-caspase domain also can be a pro-caspase form of an initiatorcaspase such as pro-caspase-1, or a peptide portion of a pro-caspasehaving initiator caspase activity potential. The oligomerizing domaincan be a polypeptide that spontaneously forms an oligomer, or that formsan oligomer in the presence of an agent that induces oligomerization. Inone embodiment, the oligomerizing domain is an FK506 binding protein(FKBP), or an FK506 binding domain of FKBP, which forms an oligomer inthe presence of a specific dimerizing agent. The oligomerizing domainalso can be a polypeptide that interacts specifically with cellularprotein in the cell, or the cellular protein binding domain of thepolypeptide. In one embodiment, the oligomerizing domain is aRas-associating domain of a Raf protein. In still another embodiment,the oligomerizing domain is a guanine exchange factor domain, whichinteracts specifically with a Ras cellular protein. A chimericpro-caspase can contain one or more additional domains, including, forexample, a protein transduction domain such as the humanimmunodeficiency virus TAT protein transduction domain, or a cellcompartmentalization domain.

The present invention also relates to an antibody that reactsspecifically with a chimeric pro-caspase. Such an antibody ischaracterized, in part, in that does not react substantially with anisolated pro-caspase domain, oligomerizing domain or other domain of achimeric pro-caspase and, therefore, can distinguish the presence of achimeric pro-caspase from, for example, a naturally occurringpro-caspase, including the pro-caspase from which the pro-caspase domainof the chimeric pro-caspase was derived. Also provided are kitscontaining such an antibody.

The present invention further relates to a polynucleotide encoding achimeric pro-caspase of the invention. The polynucleotide can becontained in a vector, which can be a cloning vector or an expressionvector, and the vector can be contained in a host cell. In oneembodiment, a polynucleotide encoding a chimeric pro-caspase iscontained in a viral expression vector. In addition, the inventionrelates to oligonucleotides, which can hybridize specifically with apolynucleotide encoding a chimeric pro-caspase. Such oligonucleotidesare characterized, at least in part, in that they do not hybridizesubstantially to nucleic acid molecules encoding individual domains ofthe chimeric pro-caspase.

The present invention also relates to a method of inducing apoptosis ina cell by providing a chimeric pro-caspase in the cell, wherein thechimeric pro-caspase includes a pro-caspase domain and an oligomerizingdomain. According to a method of the invention, the chimeric pro-caspaseforms an oligomer in the cell, thereby activating caspase activity ofthe chimeric pro-caspase and inducing apoptosis in the cell. Such amethod can be used for inducing apoptosis in a cell in vitro, or forinducing apoptosis in a cell in vivo.

A pro-caspase domain of a chimeric pro-caspase useful in a method of theinvention can be a pro-caspase form of an initiator caspase or a peptideportion of a pro-caspase having initiator caspase activity potential. Inone embodiment, the pro-caspase domain is pro-caspase-8 or a peptideportion of pro-caspase-8, which has caspase-8 activity potential. Theoligomerizing domain of a chimeric pro-caspase can be a domain thatoligomerizes spontaneously in a cell, or can be a domain that is inducedto form an oligomer in the presence of an agent that mediatesoligomerization. In one embodiment, the oligomerizing domain is FKBP,and the chimeric pro-caspase is induced to form an oligomer bycontacting the cell with an agent that induces oligomerization of FKBPs,thereby inducing apoptosis in the cell. In another embodiment, theoligomerizing domain is a polypeptide that interacts specifically withcellular protein in the cell, for example, a Raf domain, which interactsspecifically with Ras.

A method of the invention can be performed by introducing apolynucleotide encoding the chimeric pro-caspase into the cell, andexpressing the encoded chimeric pro-caspase. In performing such amethod, the polynucleotide encoding the chimeric pro-caspase can becontained in an expression vector, for example, a viral expressionvector. A method of the invention also can be performed by contactingthe cell with the chimeric pro-caspase, which can comprise a proteintransduction domain such as the human immunodeficiency virus TAT proteintransduction domain, whereby the chimeric pro-caspase is translocatedinto the cell due to the presence of the protein transduction domain.

The present invention further relates to a method of reducing theseverity of a pathologic condition in a subject, by providing cellsinvolved in the pathologic condition in the subject with a chimericpro-caspase comprising a pro-caspase domain and an oligomerizing domain,whereby the chimeric pro-caspase can oligomerize in the cell, therebyactivating caspase activity of the chimeric pro-caspase, which inducesapoptosis in the cells and reduces the severity of the pathologiccondition in the subject. The pathologic condition can be characterized,for example, by an undesirably high level of cell proliferation or by anundesirably low level of programmed cell death. In one embodiment, thepathologic condition is a neoplasia, which can be a benign neoplasia ora malignant neoplasia. In another embodiment, the pathologic conditionis an autoimmune disease, wherein the cells associated with thepathologic condition are immunocytes.

A method of the invention can be performed by providing cells of thesubject that are involved in the pathologic condition with a chimericpro-caspase ex vivo, then administering surviving cells to the subject,thereby reducing the severity of the pathologic condition in thesubject. A method of the invention also can be performed by providingcells of the subject that are involved in the pathologic condition witha chimeric pro-caspase in vivo, whereby the chimeric pro-caspase formsan oligomer in the cells, thereby activating caspase activity of thechimeric pro-caspase, inducing apoptosis in the cells, and reducing theseverity of the pathologic condition in the subject. The chimericpro-caspase, or a polynucleotide encoding the chimeric pro-caspase, canbe administered to the site of the pathologic condition, or by anymethod that provides the cells to be treated with the chimericpro-caspase. Accordingly, the invention also relates to pharmaceuticalcompositions, which can contain a chimeric pro-caspase or apolynucleotide encoding a chimeric pro-caspase.

BRIEF DESCRIPTION OF THE FIGURES

FIGS 1A and 1B show the apoptotic activity of FKBP fusions of fulllength and mutant pro-caspase-8.

FIG. 1A is a schematic diagram of the FKBP fusions of pro-caspase-8(Fkp), FK506 binding protein FKBP12; (DED), death effector domain; (p18)and (p10), subunits that form caspase-8; (d), aspartic acids at thecleavage sites for the generation of p18 and p10; (*), the active sitecysteine-to-serine mutation. cSrc myristylation signal (M) and HA andFLAG tags are also indicated.

FIG. 1B shows apoptosis induced by pro-caspase-8 fusion proteins. HeLacells were transfected with 0.125 μg of each Fkp-Casp8 plasmid and 0.25g of pRK-crmA as indicated. Percentages of specific apoptosis weredetermined as described in Example I.

FIGS. 2A and 2B show that oligomerization of the protease domain ofpro-caspase-8 induces apoptosis.

FIG. 2A shows caspase-8(180)-induced apoptosis requires oligomerizationand intrinsic protease activity. HeLa cells were transfected with 0.125μg of Fkp3, Fkp3-Casp8(180) or Fkp3-Casp8(180,C360S), together with 0.25μg of pRK-crmA or 0.125 μg of Fkp3 as indicated. Treatment of AP1510(concentration indicated) and FK506 (50 nM) was done for 10 hr asdescribed in Example I.

FIG. 2B shows pro-caspase processing is required foroligomerization-induced apoptosis. HeLa cells were transfected with0.125 μg of Fkp3, Fkp3-Casp8(206) or Fkp3-Casp8(217). AP1510 treatmentwas as described in FIG. 2A.

FIG. 3A to 3C show apoptotic activity of pro-caspase fusions with theFas extracellular domain.

FIG. 3A is a schematic diagram of pro-caspase-1, -3 and -8 fusions withthe murine Fas extracellular domain. The fusion constructs containedeither pro-caspase-8 (amino acids 182-479), full length murinepro-caspase-1, or full length human pro-caspase-3—as well as thecorresponding catalytic Cys-to-Ser mutations (not shown)—fused to theextracellular and transmembrane domain of murine Fas (FasEC). The leaderpeptide (L) and transmembrane domain (TM) of murine Fas, FLAG tag, andthe large and small subunits of each caspase are indicated.

FIG. 3B shows FasEC-mediated oligomerization of pro-caspase-8 activatesits apoptotic activity. HeLa cells were transfected with FasEC (25 ng),FasEC-Casp8(182) (25 ng), FasEC-Casp8(192, C360S) (125 ng), or pEBB-mFas(250 ng), together with pRK-crmA (250 ng) as indicated. Jo2 treatmentand X-gal staining are as described in Example I.

FIG. 3C shows FasEC-mediated oligomerization activates the apoptoticactivity of pro-caspase-1 but not pro-caspase-3. Experiments were doneas described above. The amount of plasmids used for each transfectionwas 12.5 ng for FasEC and FasEC-Casp1; 125 ng for FasEC-Casp1(C284S),FasEC-Casp3, and FasEC-Casp3(C163S); and 250 ng for pRK-crmA.

FIGS. 4A and 4B show pro-caspase processing in transfected cells.

FIG. 4A shows pro-caspase processing induced by oligomerization. 293Tcells were transfected with 1 μg of the indicated Fkp3-fusion expressionconstructs. Vehicle or 1 mM AP1510 was added 11 hr after transfection,and cell extracts were made after the indicated times and immunoblottedfor FLAG.

FIG. 4B shows processing in the presence of crmA. 293T cells werecotransfected with 1 μg of Fkp3-Casp8(180) and 1 μg of pRK5-crmA. Drugtreatment, cell extracts, and FLAG immunoblot were performed as in FIG.4A.

FIGS. 5A and 5B show pro-caspase processing in a cell-free system.

FIG. 5A shows pro-caspase processing induced by oligomerization. Theprocessing reaction was carried out with in vitro-translated,³⁵S-labeled FKBP fusions as described in Example I and visualized bySDS-PAGE and autoradiography.

FIG. 5B shows a time course of pro-caspase processing. The deduceddomain structure of the indicated bands is shown on the right.

FIG. 6 illustrates the green fluorescent protein—(GFP-) expressing MSCVretrovirus, MIG R1, and the construct encoding the Fv-caspase-8 fusionpolypeptide. DED, death effector domain; p18 and p10, the large andsmall subunits that form mature caspase-8; Flag, the FLAG epitope tag,which facilitates detection of protein by immunoblotting; IRES, internalribosome entry site; LTR, retrovirus long terminal repeats. Sequenceencoding “pro-caspase-8” is indicated. An Fv fusion that contains theentire, partial, or no prodomain can be made.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides a chimeric pro-caspase, which contains apro-caspase domain and an oligomerizing domain. As disclosed herein,oligomerization of pro-caspases induced proteolytic generation of maturecaspase subunits and activated their cell death activity (see, also,Yang et al., Mol. Cell 1:319-325 (1998a), which is incorporated hereinby reference). The present invention provides chimeric pro-caspases,which can oligomerize in a cell, thereby activating apoptosis. Chimericpro-caspases can be useful as therapeutic agents for treating, forexample, a cell proliferative disorder such as a cancer because theydirectly connect the fundamental defect in the disorders (thebiochemical signals that allow the pathologic cells to grow) to thetherapeutic goal (killing the pathologic cells). Thus, the inventionalso provides methods of reducing the severity of a pathologic conditionby providing chimeric pro-caspases in cells involved in the condition,whereby the chimeric pro-caspases oligomerize and activate apoptosis ofthe cells.

Apoptosis (programmed cell death) is a tightly controlled system forridding the body of cells that are unnecessary or undesirable. Ingeneral, apoptosis is induced by a signal that generates a cascade ofevents culminating in death of a cell and, when occurring in vivo, inremoval of the cell from the body without the generation of aninflammatory response. A prime example of a caspase cascade is found inapoptosis induced by the cell death receptor Fas (see Nagata, Cell88:355-365 (1997)). The intracellular tail of Fas interacts with theadaptor protein, FADD, which contains a death effector domain (DED) thatinteracts with homologous DED domains on pro-caspase-8(FLICE/MACH/Mch5). Recruitment of pro-caspase-8 to the receptorcompletes the death-inducing signaling complex (DISC) and activatespro-caspase-8. Active DISC formation then leads to the sequentialactivation of caspase-1-like and caspase-3-like activities.

Several polypeptides can form a complex that transmits an apoptoticsignal when the Fas/APO-1 receptor is bound (Boldin et al., Cell85:803-815 (1996); Muzio et al., Cell 85:817, 1996 ). The Fas/APOreceptor (“CD95”) is present on the surface of a wide variety of cells(Boldin et al., supra, 1996; Muzio et al., supra, 1996). The Fas/APO-1receptor and the TNF receptor are members of the TNF/nerve growth factorreceptor family and both share a region of homology designated the“death domain” (Boldin et al., supra, 1996; Muzio et al., supra, 1996).The death domain of the Fas/APO1 receptor interacts with FADD(Fas-associating protein with death domain; also known as MORT1) and RIP(receptor interacting protein), forming a complex that, when joined byCaspase-8, constitutes the Fas/APO-1 death-inducing signaling complex(Boldin et al., supra, 1996; Muzio et al., supra, 1996).

The interaction between Fas/APO-1 and FADD is mediated by theirrespective C-terminal death domains (Chinnaiyan et al., Cell 81:505-512(1995)). Caspase-8 contains two N-terminal stretches of approximately 60amino acids that are homologous to the DED of FADD (Muzio et al., supra,1996). The remainder of caspase-8 is highly homologous to the ICE/CED-3family of cysteine proteases, which induce cell death if overexpressed.A number of forms of caspase-8 have been described (Boldin et al.,supra, 1996).

The mammalian caspases are a family of cysteine proteases that cleaveafter an aspartate residue and have a central role in the programmedcell death pathway (see Henkart, Immunity 4:195-201 (1996); Salvesen andDixit, supra, 1997). Caspase-1 also processes pro-interleukin-1 and hasan important role in inflammation. Caspases normally exist in thecytoplasm as inactive pro-caspases (Salvesen and Dixit, Cell 91:443-446(1997); Thomberry and Lazebnik, Science 281:1312-1316 (1998); Alnemri etal., Cell 87:171 (1996), each of which is incorporated herein byreference). Apoptotic signals convert the precursors of a firstsubfamily of caspases, the “initiator” caspases, to mature caspases,which then activate a second subfamily of caspases, the “executioner”caspases, which cleave cellular substrates, thereby executing apoptosis.As such, the activation of initiator caspases is a key step that decidesthe fate of the cell and is subjected to intricate regulation.

Pro-caspases consist of a prodomain and a protease domain. The proteasedomain contains a large subunit and a small subunit, and two largesubunits and two small subunits interact to form a tetrameric maturecaspase. Cleavage of the protease domain at critical aspartic acidresidues releases the large and small subunits. Initiator caspasesgenerally have a long prodomain, which interacts with upstreamregulators, whereas executioner caspases generally contain a shortprodomain, which is cleaved by mature initiator caspases.

The tetrameric structure of a mature caspase, which consists of twolarge subunits of approximately 20 kDa surrounding two small subunits ofapproximately 10 kDa, was determined based on the crystal structures ofcaspase-1 and caspase-3 (Henkart, supra, 1996; Salvesen and Dixit,supra, 1997). The protease active site includes residues from bothsubunits; the large subunit contains a conserved pentapeptide (seeCohen, Biochem. J. 326:1-16 (1997), which is incorporated herein byreference). Both the large and small subunits are generated from asingle pro-caspase polypeptide by proteolytic cleavages. These cleavagesseparate the C-terminal protease domains from the N-terminal prodomainsof various lengths and also separate the two protease subunits.

Mature caspases often can process their own precursors as well as otherpro-caspases in vitro, suggesting that caspases may function in acascade (Porter et al., BioEssays 19:501-507 (1997); Salvesen and Dixit,supra, 1997). Caspases have been conceptually divided into initiatorsand executioners based on their potential roles in a cascade (Salvesenand Dixit, supra, 1997). Caspase-3 or caspase-3-like proteases areresponsible for the proteolytic cleavage of many death substrates, whichleads to the morphological changes and DNA fragmentation that are thehallmarks of apoptosis (Porter et al., supra, 1997). As such, caspase-3is regarded as an executioner caspase (Salvesen and Dixit, supra, 1997).Consistent with this hypothesis, pro-caspase-3 has a very shortprodomain and can be proteolytically activated by an upstream caspase(Muzio et al., J. Biol. Chem. 272:2952-2956 (1997)).

Prior to the present disclosure, it was not clear how a pro-caspase suchas pro-caspase 8, which initiates a cascade of caspase activation,becomes activated. Several mechanisms have been postulated, includingthe removal of an inhibitor (Fraser and Evan, Cell 85:781-784 (1996));the presence of an inducible cofactor (such as CAP3 in DISC Medema etal., EMBO J. 16:2794-2804 (1997)); or processing of pro-caspases bynoncaspases (Zhou and Salvesen, Biochem. J. 324:361-364 (1997)). Asdisclosed herein, oligomerization of pro-caspases leads toself-cleavage, which generates mature caspase enzymes and activatestheir cell death activity (see, also, Yang et al., supra, 1998a). Amajor group of cell death activators, including Apaf1 and CED-4, formhomo-oligomers, which, in turn, can induce oligomerization ofpro-caspases that associate with them. In comparison, the Bcl-2 familyof proteins exert their anti-apoptotic function by inhibiting theoligomerization of CED-4 and Apaf-1 (see Yang et al., Science 281:1312-1316 (1998b), which is incorporated herein by reference).

The present invention provides chimeric pro-caspases, which canoligomerize and activate caspase activity in a cell, and methods ofusing such chimeric pro-caspases to selectively induce apoptosis in acell. A chimeric pro-caspase is a non-naturally occurring molecule thatis engineered to contain at least a first domain, which has caspaseactivity potential, and a second domain, which has oligomerizingactivity. Upon forming an oligomer, the caspase activity of the chimericpro-caspase is activated. As used herein, the term “caspase activity”refers to an ability to cleave a polypeptide at an aspartic acid residueand initiate or propagate an apoptotic pathway. In addition, the term“caspase activity potential,” when used in reference to a pro-caspasedomain component of a chimeric pro-caspase, means that the domain has alatent ability to cleave a polypeptide at an aspartate residue andinitiate or propagate the apoptotic pathway; the latent activity ismanifest as caspase activity upon oligomerization. Caspase activitypotential of a chimeric pro-caspase can be identified by detectingcaspase activity upon oligomerization of the chimeric pro-caspase.

Methods for detecting caspase activity are disclosed herein or otherwisewell known in the art (see Example I). Such methods include, forexample, detecting characteristic structural changes in a cell such asdisruption of the cytoskeleton, cell shrinkage, membrane blebbing, ornuclear condensation due to degradation of DNA; or by detecting thecharacteristic nucleosomal degradation pattern of genomic DNA by gelelectrophoresis, or the like. Commercially available assays to detect,for example, annexin V binding to a cell in conjunction with propidiumiodide exclusion; mitochondrial membrane potential disruption; poly(ADP-ribose) polymerase activity; and the like (R & D Systems,Minneapolis Minn.; Alexis Biochemicals, San Diego Calif.) also can beused to detect caspase activity.

Caspase activity is activated upon oligomerization of a chimericpro-caspase. As used herein, the term “oligomer” refers to two or moremolecules that interact specifically with each other to form a complex.An oligomer can be a homo-oligomer, wherein each of the interactingmolecules is the same (for example, two identical chimericpro-caspases), or a hetero-oligomer, wherein the interacting moleculesinclude at least two molecules that are different from each other. Forconvenience, the molecules that interact to form an oligomer arereferred to as “binding partners,” at least one of which is a chimericpro-caspase. It should be recognized, however, that, in some embodimentsof the invention, oligomerization is not due to a direct interaction ofthe binding partners but, instead, is mediated by an agent that inducesoligomerization. For purposes of this disclosure, such an agent,although a component of the oligomer, is not considered to beencompassed within the meaning of the term “binding partner.”

As used herein, the term “interacts specifically” or “specificinteraction,” when used in reference to a chimeric pro-caspase, meansthat the chimeric pro-caspase associates directly or indirectly with itsbinding partner with a dissociation constant of at least about 1×10⁻⁶,generally at least about 1×10⁻⁷, usually at least about 1×10⁻⁸, andparticularly at least about 1×10⁻⁹ or 1×10⁻¹⁰ or less, to form anoligomeric complex. The chimeric pro-caspase can interact specificallywith another chimeric pro-caspase to form a homo-oligomer, or withmolecule other than an identical chimeric pro-caspase to form ahetero-oligomer, and the interaction can be a direct interaction of thebinding partners or can be mediated by an agent that inducesoligomerization. In general, the specific interaction of the bindingpartners is stable under physiological conditions, including, forexample, conditions that occur in a living individual such as a human orother vertebrate, or conditions generally used for culturing an organismsuch as a bacterium or yeast or cells of an organism such as mammaliancells or other cells from a vertebrate or invertebrate organism. Variouswell known methods can be used to determine whether a chimericpro-caspase interacts specifically with its binding partner to form anoligomer, including, for example, equilibrium dialysis, surface plasmonresonance, and the like.

A chimeric pro-caspase contains a pro-caspase domain and anoligomerizing domain. The pro-caspase domain of a chimeric pro-caspasecan be a pro-caspase polypeptide such as a pro-caspase form of aninitiator caspase, for example, pro-caspase-8 or pro-caspase-1, or apeptide portion of a pro-caspase having caspase activity potential (see,for example, Thomberry and Lazebnik, supra, 1998; Salvesen and Dixit,supra, 1997; Cohen, supra, 1997). As used herein, the term “peptideportion,” when used in reference to a pro-caspase, means an amino acidsequence of the pro-caspase that is less than the entire pro-caspaseamino acid sequence. Such a peptide portion of a pro-caspase can lackone or a few amino acids from the N-terminus of the naturally occurringpro-caspase, and can lack all or part of the prodomain. In general, apeptide portion of a pro-caspase useful in a chimeric pro-caspaseincludes most or all of the amino acid sequence of the C-terminus of thepro-caspase, including the portion that is cleaved to produce the small(p10) and large (p18) protease subunits, which confer caspase activity(see FIG. 1).

The oligomerizing domain provides a means through which a chimericpro-caspase oligomerizes with its binding partner. Depending on theoligomerizing domain utilized, oligomerization can be inducible or canoccur spontaneously. Where an oligomerizing domain provides forinducible oligomerization, the association of the chimeric pro-caspasewith its binding partner is mediated by an agent that inducesoligomerization. As used herein, the term “agent that inducesoligomerization” means a molecule that is required for a chimericpro-caspase to oligomerize with its binding partner. An agent thatinduces oligomerization can act in various ways. For example, the agentcan bind to an oligomerizing domain, resulting in a conformationalchange in the oligomerizing domain such that it can directly interactwith its binding partner. Such an agent acts similarly to a cofactorthat, upon binding an enzyme, produces a conformational state suitablefor substrate binding by the enzyme.

An agent that induces oligomerization also can act by mediating bindingof the chimeric pro-caspase to its binding partner. Such an agent canbe, for example, an antibody, which reacts specifically with anoligomerizing domain comprising an epitope for the antibody. An antibodygenerally can be useful to induce oligomerization of two identicalchimeric pro-caspases by binding to an identical epitope in eacholigomerizing domain of the chimeric pro-caspases, thereby inducingoligomerization. In addition, a bifunctional antibody can be used toinduce oligomerization of a chimeric pro-caspase and a binding partnerother than an identical chimeric pro-caspase, wherein one arm of thebivalent antibody reacts specifically with an epitope on theoligomerizing domain of the chimeric pro-caspase and the second arm ofthe antibody reacts specifically with an epitope on the binding partner,thereby inducing oligomerization.

An agent that induces oligomerization of a chimeric pro-caspase also canbe a small chemical molecule, which can mediate the association ofoligomerizing domains that specifically interact with the agent. Suchmolecules, referred to as “dimerizing agents” or “dimerizers,” areexemplified by natural and synthetic bivalent chemical compounds such ascyclosporin, rampamycin, coumermycin, FK506, AP1510 and AP1903, whichbind to and induce dimerization of the human FKBP12 protein (also called“FK506 binding protein” or “FKBP;” see, for example, Amara et al., Proc.Natl. Acad. Sci., USA 94:10618-10623 (1997); Clackson et al., Proc.Natl. Acad. Sci., USA 95:10437-10442 (1998); Spencer, Trends Genet.12:181-187 (1996), each of which is incorporated herein by reference).Thus, chimeric pro-caspases can be constructed having an oligomerizingdomain based on the FKBP polypeptide, or an FK506 binding domain ofFKBP, and can be induced to oligomerize by contacting them with adimerizing agent. An advantage of such chimeric pro-caspases is thatthey can be present in a cell, without activating apoptosis in the cell,and the cell can be contacted, when desired, with a membrane permeabledimerizing agent, thereby inducing oligomerization of the chimericpro-caspase, activating its caspase activity, and inducing apoptosis inthe cell.

An oligomerizing domain also can provide for spontaneous oligomerizationof a chimeric pro-caspase. As used herein, the term “spontaneous,” whenused in reference to the oligomerization of a chimeric pro-caspase,means that the chimeric pro-caspase interacts specifically with itsbinding partner upon attaining the appropriate proximity with thebinding partner. As such, no exogenous agent is required foroligomerization to occur. Oligomerizing domains that provide forspontaneous oligomerization can be derived from polypeptides thatinteract specifically with cellular proteins. For example, anoligomerizing domain can be derived from cellular Raf protein, whichinteracts specifically with a Ras cellular protein. Ras transmits itsgrowth signal, in part, by aggregating with the Raf kinase (Luo et al.,Nature 383:178-181 (1996), which is incorporated herein by reference).As such, a chimeric pro-caspase comprising an oligomerizing domain basedon the Ras-associating domain of Raf can be provided to a cancer cell,where it can interact specifically with activated Ras, thereby inducingoligomerization of the chimeric pro-caspase and activating its caspaseactivity and apoptosis in the cancer cells.

Similarly, guanine nucleotide exchange factors (GEF), which convertinactive Ras-GDP to activated Ras-GTP, also can interact specificallywith Ras in a cell. Thus, as for Raf, the Ras associating domain of aGEF can be used as an oligomerizing domain of a chimeric pro-caspase ofthe invention. GEFs are well known in the art and include, for example,Sos1, Sos2 and C3G, which are expressed in various mammalian cells, andCdc25^(Mm) and Vav, which are expressed specifically in brain cells andin hematopoietic cells, respectively (see, for example, U.S. Pat. No.5,776,689, which is incorporated herein by reference). The ability toconstruct chimeric pro-caspases having oligomerizing domains that areactive only in one or few specific cell types provides an additionalmeans to restrict caspase activity and, therefore, apoptosis to thedesired cells.

A chimeric pro-caspase can contain one or more domains in addition tothe pro-caspase domain and the oligomerizing domain. For example, achimeric pro-capase can contain a protein transduction domain such asthe human immunodeficiency virus TAT protein transduction domain(Schwarze et al., Science 285:1569-1572 (1999), which is incorporatedherein by reference). Transduction of polypeptides containing the HIVTAT protein transduction domain in vitro is rapid, occurs in aconcentration dependent manner, and does not appear to be dependent onany particular cellular receptors or transporters (Derossi et al., J.Biol. Chem. 271:18188 (1996)). Systemic administration of polypeptidescontaining the protein transduction domain in vivo resulted in deliveryof the polypeptides to all tissues, including brain, withoutcompromising the integrity of the blood brain barrier (Schwarze et al.,supra, 1999). As such, a chimeric pro-caspase comprising a proteintransduction domain is particularly useful when the chimeric pro-caspaseis to be administered directly to a cell.

A chimeric pro-caspase also can contain a cell compartmentalizationdomain, for example, a plasma membrane localization domain, a nuclearlocalization signal, a mitochondrial membrane localization signal, anendoplasmic reticulum localization signal, or the like (see, forexample, Hancock et al., EMBO J. 10:4033-4039 (1991); Buss et al., Mol.Cell. Biol. 8:3960-3963 (1988), each of which is incorporated herein byreference; see, also, U.S. Pat. No. 5,776,689). Such a domain can beuseful to target the chimeric pro-caspase to a particular compartment inthe cell, particularly the compartment in which its binding partner ispresent. For example, activated Ras generally is associated with theinner surface of the plasma membrane. Thus, a chimeric pro-caspasecontaining an oligomerizing domain based on a Ras-associating Raf domaincan further comprise a plasma membrane localization domain, therebylocalizing the chimeric pro-caspase to the site of Ras in the cell.

Where the chimeric pro-caspase comprises a polypeptide, it can beconstructed using any convenient method. Generally, a polypeptidechimeric pro-caspase, or domains comprising the chimeric pro-caspase, isexpressed from a recombinant polynucleotide encoding the chimericpro-caspase or the domains. However, the chimeric pro-caspase also canbe prepared, in whole or in part, from an isolated fragment of a proteincontaining a domain of interest, for example, a proteolytic fragmentcomprising a Ras-association domain of a Raf protein. Such an isolatedfragment comprising the oligomerizing domain can be chemically linked toa pro-caspase domain, for example, through the use of a crosslinkingagent, or by forming a disulfide or other amino acid bridge between thetwo domains, or, particularly, through a peptide bond between theC-terminus of one domain and the N-terminus of a second domain, and soon depending on the number of domains in the chimeric pro-caspase. Oneor more domains also can be chemically synthesized using well knownmethods of peptide synthesis, then linked to the other domain or domainscomprising the chimeric pro-caspase. Methods of chemical synthesis canbe particularly convenient for preparing oligopeptide domains, such as aprotein transduction domain, a cell compartmentalization domain, or arelatively small oligomerizing domain.

The domains of a chimeric pro-caspase have been exemplified generally aspolypeptide sequences. However, one or more domains of a chimericpro-caspase can be, for example, a nucleic acid molecule, apeptidomimetic, an oligosaccharide, a lipoprotein, a glycoprotein, aglycolipid, a small organic molecule, or the like. Such molecules usefulas a domain in a chimeric pro-caspase, for example, as an oligomerizingdomain, can be prepared based on a known structure or can be identifiedby screening a library of such molecules. Methods for preparing andscreening a combinatorial library of such molecules are well known inthe art and include, for example, methods of making and screening aphage display library of peptides, which can be constrained peptides(see, for example, U.S. Pat. No. 5,622,699; U.S. Pat. No. 5,206,347;Scott and Smith, Science 249:386-390 (1992); Markland et al., Gene109:13-19(1991), each of which is incorporated herein by reference); apeptide library (U.S. Pat. No. 5,264,563, which is incorporated hereinby reference); a peptidomimetic library (Blondelle et al., supra, 1995);a nucleic acid library (O=Connell et al., supra, 1996; Tuerk and Gold,supra, 1990; Gold et al., supra, 1995, each of which is incorporatedherein by reference); an oligosaccharide library (York et al., Carb.Res., 285:99-128, (1996); Liang et al., Science, 274:1520-1522, (1996);Ding et al., Adv. Expt. Med. Biol., 376:261-269, (1995),each of which isincorporated herein by reference); a lipoprotein library (de Kruif etal., FEBS Lett., 399:232-236, (1996) , which is incorporated herein byreference); a glycoprotein or glycolipid library (Karaoglu et al., J.Cell Biol., 130:567-577 (1995) , which is incorporated herein byreference); or a chemical library containing, for example, drugs orother pharmaceutical agents (Gordon et al., J. Med. Chem., 37:1385-1401(1994); Ecker and Crooke, Bio/Technology, 13:351-360 (1995) , each ofwhich is incorporated herein by reference). Domains comprised of nucleicacid molecules can be particularly useful, for example, as oligomerizingdomains, since nucleic acid molecules having binding specificity forcellular targets, including cellular polypeptides, exist naturally, andbecause synthetic molecules having such specificity can be readilyprepared and identified (see, for example, U.S. Pat. No. 5,750,342,which is incorporated herein by reference). Such domains can beengineered into the chimeric pro-caspase using, for example, a chemicallinking method specific for the particular domains.

The present invention also provides antibodies that specifically reactwith a chimeric pro-caspase. As used herein, the term “antibody” is usedin its broadest sense to include polyclonal and monoclonal antibodies,as well as antigen binding fragments of such antibodies. An antibody ofthe invention, or an antigen binding fragment thereof, is characterizedby having specific binding activity for a chimeric pro-caspase, but notfor the isolated domains comprising the chimeric pro-caspase or for anaturally occurring polypeptide from which the domain was derived. Forexample, an antibody that reacts specifically with a chimericpro-caspase comprising a pro-caspase-8 domain and a Ras-associating Rafdomain does not substantially react with an isolated pro-caspase-8 orwith an isolated Raf polypeptide.

The term “reacts specifically” or “specific binding activity,” when usedin reference to an antibody of the invention and a chimeric pro-caspase,means that an interaction of the antibody and chimeric pro-caspase has adissociation constant of at least about 1×10⁻⁶, generally at least about1×10⁻⁷, usually at least about 1×10⁻⁸, and particularly at least about1×10⁻⁹ or 1×10⁻¹⁰ or less. As such, Fab, F(ab′)₂, Fd and Fv fragments ofan antibody of the invention, which retain specific binding activity forthe chimeric pro-caspase, are included within the definition of anantibody. For purposes of the present invention, an antibody that reactsspecifically with a chimeric pro-caspase is considered to notsubstantially react with an isolated domain of the chimeric pro-caspaseor a polypeptide from which the domain is derived if the antibody has atleast a two-fold greater binding affinity, generally at least afive-fold greater binding affinity, and particularly at least a ten-foldgreater binding affinity for the chimeric pro-caspase as compared to theisolated domain or the polypeptide from which the domain was derived.

The term “antibody” as used herein includes naturally occurringantibodies as well as non-naturally occurring antibodies, including, forexample, single chain antibodies, chimeric, bifunctional and humanizedantibodies, as well as antigen-binding fragments thereof. Suchnon-naturally occurring antibodies can be constructed using solid phasepeptide synthesis, can be produced recombinantly or can be obtained, forexample, by screening combinatorial libraries consisting of variableheavy chains and variable light chains (see Huse et al., Science246:1275-1281 (1989), which is incorporated herein by reference). Theseand other methods of making, for example, chimeric, humanized,CDR-grafted, single chain, and bifunctional antibodies are well known tothose skilled in the art (Winter and Harris, Immunol. Today 14:243-246(1993); Ward et al., Nature 341:544-546 (1989); Harlow and Lane,Antibodies: A laboratory manual (Cold Spring Harbor Laboratory Press,1988); Hilyard et al., Protein Engineering: A practical approach (IRLPress 1992); Borrabeck, Antibody Engineering, 2d ed. (Oxford UniversityPress 1995); each of which is incorporated herein by reference).

Antibodies that react specifically with a chimeric pro-caspase can beraised using the chimeric pro-caspase or a peptide portion thereof as animmunogen. A non-immunogenic peptide portion of a chimeric pro-caspasecan be made immunogenic by coupling the hapten to a carrier moleculesuch bovine serum albumin (BSA) or keyhole limpet hemocyanin (KLH), orby expressing the peptide portion as a fusion protein. Various othercarrier molecules and methods for coupling a hapten to a carriermolecule are well known in the art (see, for example, by Harlow andLane, supra, 1988).

The antibodies of the invention are useful for identifying the presenceof a chimeric pro-caspase in a sample, which can be, for example, areaction mixture in which the chimeric pro-caspase was prepared, or anextract from a cell in which the chimeric pro-caspase was expressed froman encoding polynucleotide. Such antibodies also can be used to purify achimeric pro-caspase from a sample. For example, the antibodies can bebound to a solid matrix such as a chromatography matrix, then the samplecan be contacted with the antibodies. Following washing of the matrix toremove unbound material, the chimeric pro-caspases can be released fromthe antibodies and obtained in a substantially isolated form. Methodsfor attaching antibodies to solid matrices and for eluting boundantigens from such antibodies are well known in the art (see Harlow andLane, supra, 1988).

The antibodies of the invention also can be used in immunologicalassays, for example, to identify a cell containing a chimericpro-caspase. As disclosed herein, a chimeric pro-caspase can beintroduced into a cell directly, or can be expressed in the cell from apolynucleotide encoding the chimeric pro-caspase. Upon providing cellsin a subject with a chimeric pro-caspase using the methods disclosedherein, a tissue sample can be obtained from a subject, for example, bya biopsy procedure, and can be prepared for an immunoassay proceduresuch as a radioimmunoassay (RIA) or an enzyme linked immunosorbent assay(ELISA), or can be examined by microscopy using an immunohistologicalmethod.

If desired, a kit incorporating an antibody of the invention can beprepared. Such a kit can contain, in addition to the anti-chimericpro-caspase antibody, a reaction cocktail that provides the properconditions for performing an immunological assay, control samples thatcontain known amounts of the chimeric pro-caspase and, if desired, asecond antibody specific for the anti-chimeric pro-caspase antibody.Such an assay also can include a simple method for detecting thepresence or amount of a chimeric pro-caspase in a sample. Accordingly,the invention provides such kits, which contain an anti-chimericpro-caspase antibody.

Methods for raising polyclonal antibodies, for example, in a rabbit,goat, mouse or other mammal, are well known in the art. In addition,monoclonal antibodies can be obtained using methods that are well knownand routine in the art (Harlow and Lane, supra, 1988). For example,spleen cells from a mouse immunized with a chimeric pro-caspase or anepitopic fragment thereof can be fused to an appropriate myeloma cellline such as SP/02 myeloma cells to produce hybridoma cells. Clonedhybridoma cell lines can be screened using labeled chimeric pro-caspaseto identify clones that secrete anti-chimeric pro-caspase monoclonalantibodies, and hybridomas expressing antibodies having a desirablespecificity and affinity can be isolated and utilized as a continuoussource of the antibodies. Such antibodies are useful, for example, forpreparing standardized kits as described above. A recombinant phage thatexpresses, for example, a single chain anti-chimeric pro-caspase alsoprovides an antibody that can used for preparing standardized kits.

A chimeric pro-caspase or a polypeptide such as anti-chimericpro-caspase antibody can be labeled so as to be detectable using methodswell known in the art (Hermanson, “Bioconjugate Techniques” (AcademicPress 1996), which is incorporated herein by reference; Harlow and Lane,supra, 1988). For example, a chimeric pro-caspase or an antibody can belabeled with various detectable moieties including a radiolabel, anenzyme, biotin or a fluorochrome. Reagents for labeling an anti-chimericpro-caspase antibody, for example, can be included in a kit containingthe antibody or can be purchased separately from a commercial source.

The invention also provides polynucleotides encoding a polypeptidechimeric pro-caspase or a polypeptide portion of a chimeric pro-caspase.As used herein, the term “polynucleotide” is used in its broadest senseto mean two or more nucleotides or nucleotide analogs linked by acovalent bond. The polynucleotide can be single stranded or doublestranded, and can be DNA, RNA or a DNA/RNA hybrid. A polynucleotide ofthe invention generally encodes portions of at least two domains of achimeric pro-caspase, or portions of the domains. The polynucleotide isconstructed such that the domain comprising the chimeric pro-caspasegenerally are linked in frame, although they need not be contiguous andcan separated by a spacer or other amino acid sequence, which, ifdesired, can have a desirable function such as acting as a cleavage sitefor a protease. A polynucleotide that encodes all or a portion of achimeric pro-caspase is referred to as an “encoding polynucleotide.”

In general, the nucleotides comprising a polynucleotide are naturallyoccurring deoxyribonucleotides, such as adenine, cytosine, guanine orthymine linked to 2′-deoxyribose, or ribonucleotides such as adenine,cytosine, guanine or uracil linked to ribose. However, a polynucleotidealso can comprise nucleotide analogs, including non-naturally occurringsynthetic nucleotides or modified naturally occurring nucleotides. Suchnucleotide analogs are well known in the art and commercially available,as are polynucleotides containing such nucleotide analogs (Lin et al.,Nucl. Acids Res. 22:5220-5234 (1994); Jellinek et al., Biochemistry34:11363-11372 (1995); Pagratis et al., Nature Biotechnol. 15:68-73(1997), each of which is incorporated herein by reference).

The covalent bond linking the nucleotides of a polynucleotide generallyis a phosphodiester bond. However, the covalent bond also can be any ofnumerous other bonds, including a thiodiester bond, a phosphorothioatebond, a peptide-like bond or any other bond known to those in the art asuseful for linking nucleotides to produce synthetic polynucleotides(see, for example, Tam et al., Nucl. Acids Res. 22:977-986 (1994); Eckerand Crooke, BioTechnology 13:351360 (1995), each of which isincorporated herein by reference). The incorporation of non-naturallyoccurring nucleotide analogs or bonds linking the nucleotides or analogscan be particularly useful where the polynucleotide is to be exposed toan environment that can contain a nucleolytic activity, including, forexample, a tissue culture medium or upon administration to a livingsubject, since the modified polynucleotides can be less susceptible todegradation.

A polynucleotide comprising naturally occurring nucleotides andphosphodiester bonds can be chemically synthesized or can be producedusing recombinant DNA methods, using an appropriate polynucleotide as atemplate. In comparison, a polynucleotide comprising nucleotide analogsor covalent bonds other than phosphodiester bonds generally will bechemically synthesized, although an enzyme such as T7 polymerase canincorporate certain types of nucleotide analogs into a polynucleotideand, therefore, can be used to produce such a polynucleotiderecombinantly from an appropriate template (see Jellinek et al., supra,1995).

The term “oligonucleotide” also is used herein to mean two or morenucleotides or nucleotide analogs linked by a covalent bond, althoughthose in the art will recognize that oligonucleotides generally are lessthan about fifty nucleotides in length and, therefore, are a subset of“polynucleotides.” Oligonucleotides of the invention generally are atleast about 8 nucleotides in length, usually at least about 12nucleotides in length, and particularly at least about 15 or 20nucleotides in length, such that they can specifically hybridize to apolynucleotide encoding a chimeric pro-caspase under conditionsgenerally used for hybridization analysis.

The oligonucleotides of the invention are characterized, in part, inthat they hybridize to a polynucleotide encoding a chimeric pro-caspase,but not to a polynucleotide encoding an individual domain of thechimeric pro-caspase or a polypeptide from which the domain was derived.As such, the oligonucleotides can be used, for example, for Southernblot or northern blot analyses, in which case the oligonucleotide can bedetectably labeled with a moiety such as a radionuclide or afluorescent, luminescent or chemiluminescent molecule or biotin or thelike; or for PCR analysis, in which case the oligonucleotides compriseprimers. The oligonucleotides of the invention are useful, for example,for identifying a cell containing a polynucleotide encoding a chimericpro-caspase, including a cell expressing such a polynucleotide.

The invention also provides vectors containing a polynucleotide oroligonucleotide of the invention, and host cells containing suchvectors. The vector can be a cloning vector or an expression vector,depending on the purpose for which the polynucleotide is contained inthe vector. For example, the vector can be a cloning vector wherepolynucleotides encoding chimeric pro-caspases having diverseoligomerizing domains have been constructed. The cloning vectors can beused to produce a library of such polynucleotides, which then can bescreened to identify polynucleotides having a desired sequence.

The vector also can be an expression vector, which contains, in additionto an encoding polynucleotide, regulatory elements useful for expressingthe encoded polypeptide in a particular cell. An expression vector cancontain the expression elements necessary to achieve, for example,sustained transcription of the encoding polynucleotide, or theregulatory elements also can be operably linked to the polynucleotideprior to its being cloned into the vector. The term “operably linked,”when used in reference to a regulatory element, means that theregulatory element is positioned with respect to a polynucleotideencoding a chimeric pro-caspase, or a portion thereof, such that theregulatory element effects transcription or translation of the codingsequence in substantially the same manner as it does when the regulatoryelement is present in its natural position in a genome.

An expression vector (or the polynucleotide) generally contains orencodes a promoter sequence, which can provide constitutive or, ifdesired, inducible expression of the encoding polynucleotide, a poly-Arecognition sequence, and a ribosome recognition site or internalribosome entry site, and can contain other regulatory elements such asan enhancer, which can be tissue specific. The vector also containselements required for replication in a prokaryotic or eukaryotic hostsystem or both, as desired. Such vectors, which include plasmid vectorsand viral vectors such as bacteriophage, baculovirus, retrovirus,lentivirus, adenovirus, vaccinia virus, semliki forest virus andadeno-associated virus vectors, are well known and can be purchased froma commercial source (Promega, Madison Wis.; Stratagene, La Jolla Calif.;GIBCO/BRL, Gaithersburg Md.) or can be constructed by one skilled in theart (see, for example, Meth. Enzymol., Vol. 185, Goeddel, ed. (AcademicPress, Inc., 1990); Jolly, Canc. Gene Ther. 1:51-64 (1994); Flotte, J.Bioenerg. Biomemb. 25:37-42 (1993); Kirshenbaum et al., J. Clin. Invest.92:381-387 (1993), each of which is incorporated herein by reference).

Viral expression vectors can be particularly useful for introducing apolynucleotide encoding a chimeric pro-caspase into a cell, since viralvectors can infect host cells with relatively high efficiency and caninfect specific cell types. For example, a polynucleotide of theinvention can be cloned into a baculovirus vector, which then can beused to infect an insect host cell, thereby providing a means to producelarge amounts of the encoded chimeric polypeptide. In addition, theviral vector can be derived from a virus that infects vertebrate hostcells, particularly mammalian host cells. Viral vectors can beparticularly useful for introducing a polynucleotide encoding a chimericpro-caspase into a mammalian cell, wherein, upon expression of thechimeric pro-caspase, oligomerization can occur, thereby activating thecaspase activity and inducing apoptosis in the cell. Viral vectors havebeen developed for use in mammalian systems and include, for example,retroviral vectors, other lentivirus vectors such as those based on thehuman immunodeficiency virus (HIV), adenovirus vectors, adeno-associatedvirus vectors, herpesvirus vectors, vaccinia virus vectors, and the like(see Miller and Rosman, BioTechniques 7:980-990 (1992); Anderson et al.,Nature 392:25-30 Suppl. (1998); Verma and Somia, Nature 389:239-242(1997); Wilson, New Engl. J. Med. 334:1185-1187 (1996), each of which isincorporated herein by reference).

When retroviruses, for example, are used for gene transfer, replicationcompetent retroviruses theoretically can develop due to recombination ofretroviral vector and viral gene sequences in the packaging cell lineutilized to produce the retroviral vector. Packaging cell lines in whichthe production of replication competent virus by recombination has beenreduced or eliminated can be used to minimize the likelihood that areplication competent retrovirus will be produced. All retroviral vectorsupernatants used to infect cells are screened for replication competentvirus by standard assays such as PCR and reverse transcriptase assays.Retroviral vectors allow for integration of a heterologous gene into ahost cell genome, which allows for the gene to be passed to daughtercells following cell division.

A polynucleotide, which can be contained in a vector, can be introducedinto a cell by any of a variety of methods known in the art (Sambrook etal., “Molecular Cloning: A laboratory manual” (Cold Spring HarborLaboratory Press 1989); Ausubel et al., “Current Protocols in MolecularBiology” (John Wiley and Sons, Baltimore, Md. 1994), each of which isincorporated herein by reference). Such methods include, for example,transfection, lipofection, microinjection, electroporation and infectionwith recombinant vectors, and can include the use of liposomes,microemulsions or the like, which can facilitate introduction of thepolynucleotide into the cell and can protect the polynucleotide fromdegradation prior to its introduction into the cell.

Introduction of a polynucleotide into a cell by infection with a viralvector is particularly advantageous in that it can efficiently introducethe nucleic acid molecule into a cell ex vivo or in vivo (see, forexample, U.S. Pat. No. 5,399,346, which is incorporated herein byreference). Moreover, viruses are very specialized and typically infectand propagate in specific cell types. Thus, their natural specificitycan be used to target the nucleic acid molecule contained in the vectorto specific cell types. As such, a vector based on an HIV can be used toinfect T cells, a vector based on an adenovirus can be used, forexample, to infect respiratory epithelial cells, a vector based on aherpesvirus can be used to infect neuronal cells, and the like. Othervectors, such as adeno-associated viruses can have greater host cellrange and, therefore, can be used to infect various cell types, althoughviral or non-viral vectors also can be modified with specific receptorsor ligands to alter target specificity through receptor mediated events.

As disclosed herein, oligomerization of pro-caspases induced proteolyticgeneration of mature caspase subunits and activated their cell deathactivity (see, also, Yang et al., supra, 1998a, 1998b). Deletion of theprotein interaction motif, DED (“death effector domain”), frompro-caspase-8 greatly suppressed its apoptotic activity (see Example I).Cell death activity was restored by oligomerizing pro-caspase-8 proteasedomains using two heterologous inducible oligomerization systems.Induced oligomerization also activated the apoptotic activity ofpro-caspase-1, but not pro-caspase-3. In vitro, oligomerization resultedin pro-caspase processing to form the mature caspase subunits; thisprocessing required the intrinsic caspase activity of zymogens andproceeded via a previously unknown order of cleavage events (Example I).

Two inducible oligomerization systems were used to demonstrate thatoligomerization activates pro-caspase processing, thereby activatingcaspase activity. Pro-caspase-8 products obtained in a cell-freeprocessing system indicated that the prodomain is first separated fromthe protease domain, followed by the separation of the two proteasesubunits (see Example I). This order of cleavages is distinct from thatobserved when pro-caspase-8 was used as a substrate for active DISC(Medema et al., supra, 1997). Thus, pro-caspase processing byoligomerization occurs through a distinct mechanism from that involvedin processing of a pro-caspase by a mature caspase as occurs in othersteps of the cascade.

Oligomerization-induced activation likely reflects the in vivo situationfor pro-caspase-8, which is known to occur at caspase sites (Medema etal., supra, 1997). Oligomerization-induced processing was inhibited bythe caspase inhibitor, Z-DEVD (see Example I; FIG. 5A), and wasabrogated by deletion of the recognition site at amino acid 216 (FIG.4A, FIG. 5A). In addition, the processed products correspond to theintermediates detected in cells undergoing Fas-induced apoptosis (Medemaet al., supra, 1997). Furthermore, by making a FasEC-caspase-8 fusion,the intervening protein interaction motifs for the in vivoFas-FADD-caspase-8 connection were by-passed. FasEC-caspase-8 killedcells in a Jo2-dependent manner, strikingly similar to Fas-mediated celldeath (FIG. 3B). Therefore, the in vivo function of many proteins in theFas receptor complex is likely to facilitate and regulateoligomerization of pro-caspase-8.

Oligomerization of pro-caspases can be a general mechanism in initiatingcaspase cascades. Caspases have been divided into three major groups—acaspase-8-like group, a caspase-1-like group, and a caspase-3-likegroup—based on their substrate specificities (Thornberry et al., supra,1997). As disclosed herein, oligomerization induced the activation ofpro-caspase-8 and pro-caspase-1 (see Example I). A caspase-3-likeprotease, caspase-2 (Ich-1), binds to the death adaptor RAIDD via itsprodomain and is recruited to TNF receptor-1 (Duan and Dixit, Nature385:86-89 (1997)). Membrane recruitment and oligomerization ofpro-caspase-2 then can lead to autoproteolytic activation in a fashionsimilar to that found for pro-caspase-8. In comparison, inducedoligomerization of pro-caspase-3 did not enhance its cell deathactivity. These results indicate that prodomain structure, rather thansubstrate specificity, can determine the ability of a pro-caspase to beactivated by oligomerization. Furthermore, this difference betweenpro-caspase-8 and pro-caspase-1 as compared to pro-caspase-3 reinforcesthe conceptual division of initiator and executioner caspases, andindicates that oligomerization-induced activation is a property of theinitiator caspases.

Controlling the oligomerization state of pro-caspases can be a criticalregulatory event in the cellular decision for life or death. Specificadaptor proteins that interact with the prodomains of variouspro-caspases may allow distinct apoptotic stimuli to engage the celldeath machinery by inducing pro-caspase oligomerization. A logical stepin inducing pro-caspase oligomerization is to bring them near membranes,thus reducing their movement from three dimensions to two dimensions andincreasing their local concentration. A recent study showed thatpro-caspase-8 can be recruited to the endoplasmic reticulum (ER)membrane through an ER protein, p28 Bap31 (Ng et al., J. Cell Biol.139:327-338 (1997), which is incorporated herein by reference). Celldeath effectors such as CED-4, Bcl-2, and cytochrome c may exert theireffects through regulating oligomerization of pro-caspases. TheCaenorhabditis elegans death effector CED-4 and its mammalian homologApaf-1 interact with the zymogen form of CED-3 and caspase-9,respectively (Hengartner, Nature 388:714-715 (1997); Li et al., Cell91:479-489 (1997)). CED-4 also associates with the cell death inhibitorCED-9, while Apaf-1 associates with the cell death initiator cytochromec (Hengartner, supra, 1997). It is likely that additional regulatorystrategies also control the activity of caspases.

Oligomerization-induced activation of pro-caspases is reminiscent of theactivation of receptor tyrosine kinases. Oligomerization of receptortyrosine kinases leads to intermolecular cross-phosphorylation, whichcan increase their kinase activity and enhance their interaction withcellular proteins (Ullrich and Schlessinger. Cell 61:203-212 (1990)). Ina similar manner, autoproteolytic processing of pro-caspases producesmature caspases that possess greater enzymatic activity.Oligomerization-induced autoproteolysis is an established mechanism inactivating the complement protease cascade. As disclosed herein, asimilar mechanism is used to initiate an intracellular protease cascadefor programmed cell death, and provides an additional example ofoligomerization in activating signal transduction pathways.

The discovery that cell growth and cell death are controlled by similarmechanisms provides a means by which growth signals can be turned intodeath signals (and vice versa) by straight-forward manipulations.Accordingly, the present invention provides a method of inducingapoptosis in a cell by providing a chimeric pro-caspase in the cell,whereby the chimeric pro-caspase forms an oligomer in the cell, therebyactivating caspase activity of the chimeric pro-caspase and inducingapoptosis in the cell. Such a method can be used for inducing apoptosisin a cell in vitro, or for inducing apoptosis in a cell in vivo.

As used herein, the term “providing a chimeric pro-caspase in a cell”means either that a chimeric pro-caspase is introduced into the cell orthat a polynucleotide encoding a chimeric pro-caspase is introduced intothe cell, after which the encoded chimeric pro-caspase is expressed inthe cell. Well known methods can be used for determining that a chimericpro-caspase is provided in a cell. Where the chimeric pro-caspase isintroduced directly into the cells or is expressed from a polynucleotideintroduced into the cells, its presence in the cell can be detecteddirectly using an antibody that reacts specifically with the chimericpro-caspase. For example, a cell extract can be prepared from the cellsand a western blot analysis or an immunoassay such as an RIA or ELISAcan be performed.

If desired, the chimeric pro-caspase can comprise a detectable markersuch as a FLAG epitope, thus allowing the use of an anti-FLAG antibodyto detect the presence of the chimeric pro-caspase in the cell (see, forexample, Hopp et al., BioTechnology 6:1204 (1988); U.S. Pat. No.5,011,912, each of which is incorporated herein by reference). Otherdetectable markers such as a c-myc epitope, which can be detected usingan antibody specific for the epitope; a polyhistidine sequence, whichcan be detected using a divalent cation such as nickel ion, cobalt ion,or the like; biotin, which can be detected using streptavidin or avidin;glutathione S-transferase, which can be detected using glutathione; orthe like also can be used to identify the presence of a chimericpro-caspase in a cell. Such markers can provide the additional advantagethat they can be used as a tag to facilitate isolation of thepro-caspase, for example, where it is desired to obtain a relativelypurified chimeric pro-caspase preparation.

Where the chimeric pro-caspase is expressed from a polynucleotide, whichis introduced into the cells, the presence of the chimeric pro-caspasein the cell can be detected indirectly by performing northern blotanalysis using an oligonucleotide probe that hybridizes specificallywith the encoding polynucleotide and detecting the presence of the anmRNA encoded by the introduced polynucleotide. An oligonucleotide primeralso can be used and PCR can be performed to detect the presence of theintroduced polynucleotide, or of mRNA expressed from the polynucleotide.If desired, the polynucleotide encoding the chimeric pro-caspase canfurther comprise a nucleotide sequence encoding a detectable marker suchas green fluorescent protein (see FIG. 6), θ-galactosidase, luciferase,or the like, thus facilitating detection of the expressed chimericpro-caspase. Such detectable markers can be particularly useful becausecells containing the chimeric pro-caspase can be detected visually, andbecause such markers can facilitate high throughput analysis of cells,for example, where it is desired to use a method such as fluorescenceactivated cell sorting to separate cells containing the chimericpro-caspase from those lacking it.

Although chimeric pro-caspases generally are large polypeptides, whichdo not readily traverse a cell membrane, various methods are known forintroducing a polypeptide into a cell. The selection of a method forintroducing the chimeric pro-caspase into a cell will depend, in part,on the characteristics of the target cell, into which the chimericpro-caspase is to be provided. For example, where the target cells, or afew cell types including the target cells, express a receptor, which,upon binding a particular peptide ligand, is internalized into the cell,the chimeric pro-caspase can include a domain corresponding to thepeptide ligand. Upon binding to the receptor, the chimeric pro-caspaseis translocated into the cell by receptor-mediated endocytosis. Achimeric pro-caspase also can be contained in a liposome or formulatedin a lipid complex, which can facilitate entry of the chimericpro-caspase into the cell. A chimeric pro-caspase also can be introducedinto a cell by engineering the chimeric pro-caspase to contain a proteintransduction domain such as the human immunodeficiency virus TAT proteintransduction domain, which facilitates translocation of the chimericpro-caspase into the cell (see Schwarze et al., supra, 1997).

A method of the invention also can be performed by introducing apolynucleotide encoding the chimeric pro-caspase into the cell, andexpressing the encoded chimeric pro-caspase. The encodingpolynucleotide, which can be contained in an expression vector, forexample, a viral expression vector, can be contacted directly with thecells, or can be contained in a liposome or formulated in a lipidcomplex, microemulsion, or the like, which can facilitate introductioninto the cell. Upon expression, the chimeric pro-caspase can oligomerizespontaneously or can be induced to oligomerize, thereby activatingcaspase activity of the chimeric pro-caspase and inducing apoptosis inthe cell.

A method of the invention can be useful for ridding a mixed populationof cells of one or more undesirable populations of cells. For example,the method can be used to selectively kill a undesirable population ofcells in culture that threaten to overgrow a desirable population ofcells. The chimeric pro-caspases can be provided selectively to theundesirable population of cells based, for example, on the use of viralvector that infects the undesirable, but not the desirable population ofcells, or on a higher transfection efficiency of the undesirable cellsas compared to the desirable cells, or some other distinguishingcharacteristic of the undesirable cells such that the chimericpro-caspase or an encoding polynucleotide preferentially is taken up bythe undesirable cells. Alternatively, the chimeric pro-caspases can bedesigned to oligomerize selectively in the undesirable cells based, forexample, on the presence of an oligomerizing domain in the chimericpro-caspase that spontaneously oligomerizes with a polypeptide that isexpressed only, or at a higher level, in the undesirable cells.

Where the cells in which apoptosis is to be induced are obtained from orare present in a subject suffering from a pathologic condition, a methodof the invention provides a means to treat the subject. Accordingly, thepresent invention provides a method of reducing the severity of apathologic condition in a subject, by providing cells involved in thepathologic condition in the subject with a chimeric pro-caspase, wherebythe chimeric pro-caspase can oligomerize in the cell, thereby activatingcaspase activity of the chimeric pro-caspase, inducing apoptosis in thecells, and reducing the severity of the pathologic condition in thesubject.

The term “pathologic condition” is used herein to refer to any disorderthat is characterized, at least in part, by the presence of cells thatare deleterious to the health of a subject. The pathologic condition canbe, for example, a cell proliferative disorder that is characterized, inpart, by a loss of growth regulation, which can be due to an undesirablyhigh level of cell proliferation or to an undesirably low level ofprogramned cell death, or can be characterized by cells that do notexhibit a loss of growth control, but instead exhibit a dysregulation ofcell function that contributes to the pathologic condition. Referenceherein to cells as being “associated with” or “involved in” a pathologicconditions means those cells that primarily contribute to the signs andsymptoms of the pathologic condition and in which it is desired toinduce apoptosis. Generally, the cells associated with the pathologiccondition correspond to cells that normally are present in the subject.However, the cells can be, for example, transplanted cells that areinvolved in a graft-versus-host response and, therefore, are involved ina pathologic condition.

The use of a chimeric pro-caspase for treating a pathologic conditionsuch as cancer provides a significant therapeutic advantage overconventional cancer therapies, including surgery, chemotherapy, andradiation therapy, because the chimeric pro-caspases can be effectiveagainst disseminated disease and can produce minimal toxic side effectstoward normal tissue. Current cancer therapies approaches this goalempirically and indirectly. Surgery can be an effective treatment, inthat it can remove a tumor in bulk. However, surgery is only effectiveif the cancer cells have not spread from the primary site. In addition,surgery can produce significant morbidity. Radiation therapy andchemotherapy can be used to treat more disseminated cancers damage, butgenerally act by killing rapidly dividing cells, which includes bothcancerous cells and normal cells. As a result, these therapies havedeleterious effects on rapidly renewing tissues such as the bone marrowand gastrointestinal tract, which often limits the amount of treatmentthat can be administered. As disclosed herein, chimeric pro-caspases arerationally designed and, therefore, can be engineered, for example, totarget a component of a biochemical pathway involved in a cell involvedin a pathologic condition, for example, cancer cells. As such, chimericpro-caspases of the invention provide a more specific therapeutic agentthat is less likely to produce significant toxic side effects.

Chimeric pro-caspases also can be more potent therapeutic agents thancurrent treatments because radiation therapy and chemotherapy, forexample, depend on damaged cancer cells to respond by initiatingprogrammed cell death. However, cancer cells frequently acquireadditional mutations in the damage response circuit and become resistantto treatment. As a result, many types of cancers, particularly in theirlater stages, become refractory to chemotherapy and radiation therapy.In contrast, chimeric pro-caspases have enzymatic activity that directlyinduces apoptosis, thus by-passing potential mutations that canotherwise interfere with the induction of programmed cell death. Infact, active caspases can efficiently kill cancer cells even after thecells have become resistant to a chemotherapeutic treatment.

A method of the invention can reduce the severity of a pathologiccondition in a subject by inducing apoptosis in cells associated withthe pathologic condition in the subject. As used herein, the term“reduce the severity of a pathologic condition” means that particularsigns or symptoms associated with the pathologic condition qualitativelyor quantitatively are lessened. The signs or symptoms to be monitoredwill be characteristic of a particular pathologic condition and will bewell known to skilled clinician, as will the methods for monitoring thesigns and conditions. For example, where the pathologic condition is amalignant neoplasia, the skilled clinician can monitor the size orgrowth rate of a tumor using diagnostic imaging methods, and candetermine that the severity of the condition is reduced by detecting adecreased growth rate or decreased size of the tumor. In addition, theclinician can monitor the level of an enzyme, antigen or otherbiological product that is prognostic of the status of the condition,for example, prostate specific antigen, carcinoembryonic antigen, or thelike, as relevant. The clinician also can identify a reduction in theseverity of the condition simply by the treated subject indicating thathe or she feels less nausea, or more strength, or just generally feelsbetter. Where the pathologic condition is vascular stenosis, theclinician can determine whether the severity of the condition is reducedby performing an angiogram, by measuring blood flow through the involvedblood vessel, by examining the level of fatigue exhibited by the patientfollowing a particular task, or the like. Where the pathologic conditionis an autoimmune disease, the clinician can determine theimmunoreactivity of the patient's immunocytes in an appropriate in vitroimmunologic assay, can biopsy the involved tissue and examine thehistopathologic or immunohistologic status of the tissue, can examinethe mobility of joint involved in the condition or the pain associatedtherewith, or the like.

The severity of various pathologic conditions can be reduced using amethod of the invention. Such pathologic conditions include, forexample, malignant neoplasms such as a carcinoma or fibrosarcoma of thebreast, prostate, lung, liver, colon, rectum, kidney, stomach, pancreas,ovary, bladder, cervix, uterus, or brain; a glioblastoma; anastrocytoma; or other malignant neoplasm, including metastatic lesions;and benign neoplasms such as benign prostatic hyperplasia, meningioma,hemangioma and angiofibroma. Other pathologic conditions amenable totreatment using a method of the invention include, for example,conditions that are associated with undesirably high levels ofangiogenesis such as occurs in diabetic retinopathy, comeal graftneovascularization and neovascular glaucoma, as well as inflammatoryconditions such as synovitis, dermatitis and bacterial infection orother infectious conditions, which can be associated with undesirableangiogenesis; endometriosis; arterial stenosis, including, for example,coronary artery stenosis and restenosis, which can occur following anangioplasty procedure; epithelial conditions such as psoriasis; and theformation of hypertrophic scars such as keloids or of vascular adhesionsas occur in granulation tissues, including burns, pyogenic granuloma,and the like. In addition, autoimmune diseases such as rheumatoidarthritis, systemic lupus erythematosis, and the like, which arecharacterized, in part, by the presence in the subject of dysregulatedimmunocytes, are amenable to treatment using a method of the invention.

A method of the invention can be performed by providing cells of thesubject that are involved in the pathologic condition with a chimericpro-caspase ex vivo, then administering surviving cells to the subject,thereby reducing the severity of the pathologic condition in thesubject. Autoimmune diseases, for example, are characterized by thepresence in the subject of immunocytes that are dysregulated, in thatthey do not recognize a normal epitope expressed in a subject, treat theepitope as a foreign antigen, and generate the production ofautoantibodies against the antigen and, therefore, against the subject.Such immunocytes, which generally are B cells, are generated fromprecursor cells, including stem cells and memory cells, which arepresent in the bone marrow, spleen or lymph nodes or circulate in theblood or lymph fluid of the subject. As such, bone marrow cells andcells from the spleen or lymph nodes, for example, can be obtained fromthe patient and placed in appropriate cell culture conditions, and canbe contacted with chimeric pro-caspases of the invention or withpolynucleotides encoding the chimeric pro-caspases as desired.

In such a method, the chimeric pro-caspases are designed such that theyoligomerize only in the cells in which apoptosis is to be induced. Forexample, the autoimmune disease can be characterized, in part, by theexpression of antibodies that are reactive against an epitope in thesubject. Where the epitope is known, the oligomerizing domain of thechimeric pro-caspase can include the epitope, which further can comprisea protein transduction domain if the chimeric pro-caspase is to beadministered to the cells. Where the antigen is not known, but theantibodies can be isolated, an anti-idiotypic antibody can be preparedand can serve the function of an oligomerizing domain. A goal of usingsuch chimeric pro-caspases is that the deleterious antibodies can induceoligomerization of the chimeric pro-caspases only in the cells thatproduce the antibody, thereby specifically killing the cells associatedwith the pathology, while sparing normal cells. Since the antibodiesgenerally are confined to particular compartments in the antibodyproducing cells, the chimeric pro-caspase further comprises theappropriate cell compartmentalization domain, thus localizing thechimeric pro-caspase in proximity to the antibodies. Apoptosis of thecells that produce the deleterious antibodies occurs, after which thesurviving cells can be reinfused into the patient, thereby reducing theseverity of the autoimmune disease.

In treating an autoimmune disease as disclosed above, the cells can beprovided with a polynucleotide encoding the chimeric pro-caspase and thepolynucleotide can become integrated into the genome of stem cells orother B cell precursor cells of the subject. In such a case, it can bepreferable to construct the polynucleotide such that it is operablylinked to an expressible regulatory element, for example, a B cellspecific regulatory element. Using such a construct, any immunocytesthat are newly generated from the stem cells and otherwise wouldcontribute to the pathologic condition are killed upon maturation to thestage in which antibody production occurs, since the antibodies willinduce oligomerization of the expressed chimeric pro-caspase.

A similar method can be used to treat virally infected cells such as HIVinfected T cells. In such a method, the chimeric pro-caspase is designedto contain an oligomerizing domain that specifically interacts with anHIV polypeptide that is expressed in the virally infected cell, therebyinducing apoptosis in T cells that are infected with HIV. If desired,apoptosis of the T cells containing the chimeric pro-caspase can occurin vitro, after which the surviving cells are administered back into thesubject, or the T cells can be reinfused into the subject and apoptosisof the cells can occur in the subject. If desired, the encodingpolynucleotide can be operably linked to an HIV regulatory element suchthat expression of the chimeric pro-caspase occurs in concert withexpression of the HIV polypeptide binding partner. Such a methodconveniently restricts apoptosis to HIV infected cells that otherwisewould produce infective viruses. The encoding polynucleotide also can becloned into a viral expression vector derived from HIV, thusfacilitating infection of T cells, which also are the target cells forHIV infection. Such an HIV viral vector containing the encodingpolynucleotide can be particularly useful for an in vivo gene therapyprocedure. Thus, a method of the invention can be performed by providingcells of the subject that are involved in the pathologic condition witha chimeric pro-caspase in vivo, whereby the chimeric pro-caspase formsan oligomer in the cells, thereby activating caspase activity of thechimeric pro-caspase, inducing apoptosis in the cells, and reducing theseverity of the pathologic condition in the subject.

A chimeric pro-caspase, or a polynucleotide encoding the chimericpro-caspase, can be administered to the site of the pathologiccondition, or by any method that provides the cells associated with thepathologic condition with the chimeric pro-caspase. For administrationto a living subject, a chimeric pro-caspase generally is formulated in apharmaceutical composition suitable for administration to the subject.Thus, the invention further provides pharmaceutical compositions, whichcontain an agent and a chimeric prq-caspase or a polynucleotide encodinga chimeric pro-caspase in a pharmaceutically acceptable carrier. Assuch, the chimeric pro-caspases of the invention and the polynucleotidesencoding the chimeric pro-caspases are useful as medicaments fortreating a subject suffering from a pathological condition.

Pharmaceutically acceptable carriers are well known in the art andinclude, for example, aqueous solutions such as water or physiologicallybuffered saline or other solvents or vehicles such as glycols, glycerol,oils such as olive oil or injectable organic esters. A pharmaceuticallyacceptable carrier can contain physiologically acceptable compounds thatact, for example, to stabilize or to increase the absorption of theconjugate. Such physiologically acceptable compounds include, forexample, carbohydrates, such as glucose, sucrose or dextrans,antioxidants, such as ascorbic acid or glutathione, chelating agents,low molecular weight proteins or other stabilizers or excipients. Oneskilled in the art would know that the choice of a pharmaceuticallyacceptable carrier, including a physiologically acceptable compound,depends, for example, on the physico-chemical characteristics of thetherapeutic agent, for example, on whether a chimeric pro-caspasepolypeptide or a polynucleotide encoding the chimeric pro-caspase is tobe administered; and on the route of administration of the composition,which can include, for example, orally or parenterally such asintravenously, and by injection, intubation, or other such method knownin the art. The pharmaceutical composition also can contain an agentsuch as a diagnostic agent, nutritional substance, toxin, or therapeuticagent, for example, a cancer chemotherapeutic agent.

The chimeric pro-caspase or encoding polynucleotide can be incorporatedwithin an encapsulating material such as into an oil-in-water emulsion,a microemulsion, micelle, mixed micelle, liposome, microsphere or otherpolymer matrix (see, for example, Gregoriadis, Liposome Technology, Vol.1 (CRC Press, Boca Raton, Fla. 1984); Fraley, et al., Trends Biochem.Sci., 6:77 (1981), each of which is incorporated herein by reference).Liposomes, for example, which consist of phospholipids or other lipids,are nontoxic, physiologically acceptable and metabolizable carriers thatare relatively simple to make and administer. “Stealth” liposomes (see,for example, U.S. Pat. Nos. 5,882,679; 5,395,619; and 5,225,212, each ofwhich is incorporated herein by reference) are an example of suchencapsulating materials particularly useful for preparing apharmaceutical composition of the invention and for practicing a methodof the invention, and other “masked” liposomes similarly can be used,such liposomes extending the time that the therapeutic agent remain inthe circulation. Cationic liposomes, for example, also can be modifiedwith specific receptors or ligands (Morishita et al., J. Clin. Invest.,91:2580-2585 (1993), which is incorporated herein by reference). Inaddition, a nucleic acid molecule can be introduced into a cell using,for example, adenovirus-polylysine DNA complexes (see, for example,Michael et al., J. Biol. Chem. 268:6866-6869 (1993), which isincorporated herein by reference).

The route of administration of a pharmaceutical composition of theinvention will depend, in part, on the chemical structure of thechimeric pro-caspase. Polypeptides and polynucleotides, for example, arenot particularly useful when administered orally because they can bedegraded in the digestive tract. However, methods for chemicallymodifying polypeptides, for example, to render them less susceptible todegradation by endogenous proteases or more absorbable through thealimentary tract are well known (see, for example, Blondelle et al.,supra, 1995; Ecker and Crook, supra, 1995). In addition, the chimericpro-caspases can be prepared from domains that are identified fromlibraries of peptides containing D-amino acids; peptidomimeticsconsisting of organic molecules that mimic the structure of acoagulation factor; or peptoids such as vinylogous peptoids, using thescreening methods disclosed herein.

A pharmaceutical composition comprising a chimeric pro-caspase orencoding polynucleotide can be administered to an individual by variousroutes including, for example, orally or parenterally, such asintravenously, intramuscularly, subcutaneously, intraorbitally,intracapsularly, intraperitoneally, intrarectally, intracisternally orby passive or facilitated absorption through the skin using, forexample, a skin patch or transdermal iontophoresis, respectively.Furthermore, the pharmaceutical composition can be administered byinjection, intubation, orally or topically, the latter of which can bepassive, for example, by direct application of an ointment, or active,for example, using a nasal spray or inhalant, in which case onecomponent of the composition is an appropriate propellant. Apharmaceutical composition also can be administered to the site of apathologic condition, for example, intravenously or intra-arteriallyinto a blood vessel supplying a tumor.

The total amount of a chimeric pro-caspase or encoding polynucleotide tobe administered can be administered to a subject as a single dose,either as a bolus or by infusion over a relatively short period of time,or can be administered using a fractionated treatment protocol, in whichmultiple doses are administered over a prolonged period of time. Oneskilled in the art would know that the amount of the pharmaceuticalcomposition to treat a pathologic condition in a subject depends on manyfactors including the age and general health of the subject as well asthe route of administration and the number of treatments to beadministered. In view of these factors, the skilled artisan would adjustthe particular dose as necessary. In general, the formulation of acomposition of the invention and the routes and frequency ofadministration are determined, initially, using Phase I and Phase IIclinical trials.

The pharmaceutical composition can be formulated for oral formulation,such as a tablet, or a solution or suspension form; or can comprise anadmixture with an organic or inorganic carrier or excipient suitable forenteral or parenteral applications, and can be compounded, for example,with the usual non-toxic, pharmaceutically acceptable carriers fortablets, pellets, capsules, suppositories, solutions, emulsions,suspensions, or other form suitable for use. The carriers, in additionto those disclosed above, can include glucose, lactose, mannose, gumacacia, gelatin, mannitol, starch paste, magnesium trisilicate, talc,corn starch, keratin, colloidal silica, potato starch, urea, mediumchain length triglycerides, dextrans, and other carriers suitable foruse in manufacturing preparations, in solid, semisolid, or liquid form.In addition auxiliary, stabilizing, thickening or coloring agents andperfumes may be used, for example a stabilizing dry agent such astriulose (see, for example, U.S. Pat. No. 5,314,695).

A chimeric pro-caspase or an encoding polynucleotide can be administeredto a subject in order to reduce the severity of a pathologic conditionin the subject by inducing apoptosis of cells involved in the pathologiccondition. For example, the cells associated with a pathologic conditioncan be characterized, in part, by the misexpression of a cell growthprotein, and the chimeric pro-caspase can be designed such thatoligomerization is effected due to its interacting specifically with thecell growth protein. Cancer, for example, fundamentally is a disease ofuncontrolled cell growth. In many cases, the cancer cells harboroncogenic mutations that cause the switch for cell growth to be stuck inthe “on” position. In particular, key protein kinases that are involvedcell proliferation can be maintained in the aggregated state and,therefore, remain activated. Accordingly, the elements of such proteinkinases can be used to prepare a chimeric pro-caspase of the invention,which can oligomerize with the protein kinase in the cancer cell andinduce a apoptosis in the cells.

A chimeric pro-caspase useful in treating a cancer patient, for example,can comprise an oligomerizing domain that interacts specifically with aRas protein expressed in the cancer cells. Mutated Ras oncogenes arepresent in approximately thirty percent of human cancers. Morespecifically, Ras is mutated in about 25% to 30% of lung cancers, 50% ofcolon cancers, and 90% of pancreatic cancers, which are the first, thirdand fourth leading causes, respectively, of cancer death in the UnitedStates. In addition, even in cancers that are not characterized by overtRas mutations, elevated Ras activity contributes to tumor growth. Forexample, the Her2/neu oncogene, which is overexpressed in aggressivebreast cancers, triggers cancer cells to divide by signaling throughRas.

Ras transmits its growth signal, in part, by aggregating with the Rafkinase (Luo et al., Nature 383:178-181 (1996), which is incorporatedherein by reference). As such, a chimeric pro-caspase comprising anoligomerizing domain based on a Ras-associating domain of Raf canrespond specifically to activated Ras in cancer cells. Similarly, achimeric pro-caspase can comprise an oligomerizing domain based on aRas-associating domain of a guanine nucleotide exchange factors GEF canoligomerize with Ras in a cell, thereby activating apoptosis in thecell. Such chimeric pro-caspases, which can further comprise, forexample, a membrane localization domain (see U.S. Pat. No. 5,776,689),can kill cells characterized, at least in part, by excessive Rasactivity, thereby providing a therapeutic benefit for patients sufferingfrom a number of common human cancers.

For treatment of a subject in vivo, a chimeric pro-caspase can comprise,for example, a peptide ligand domain, which binds a specific receptorexpressed by the target cell (i.e., the cell involved in the pathologiccondition); a protein transduction domain, which facilitatestranslocation into the cell; a cell compartmentalization domain, whichlocalizes the chimeric pro-caspase to the appropriate cell compartment,or the like. In performing a method of the invention, the chimericpro-caspase or encoding polynucleotide can be administered alone to thesubject, or can be administered in combination with another therapyuseful for treating the condition. For example, as disclosed herein, apolynucleotide encoding a chimeric pro-caspase comprising anoligomerizing domain that interacts specifically with Ras can beadministered to a subject having a cancer characterized, in part, byover-expression or increased activity of Ras, thereby reducing theseverity of the cancer. In addition, the subject can be treated usingmore routine methods, including, for example, by treatment with anappropriate chemotherapeutic agent.

A method of the invention similarly can be useful for reducing theseverity of a viral infection, which are characterized, in part, by theexpression of viral proteins in cells associated with the pathologiccondition. For such a method, the chimeric pro-caspase is designed withan oligomerizing domain that interacts specifically with a polypeptideexpressed by the virus or in response to viral infection of the cell. Assuch, the chimeric pro-caspase only oligomerizes in the virally infectedcells, thereby restricting apoptosis only to those cells involved in thepathology.

In one embodiment, the invention provides a method of gene therapy. Anadvantage of a gene therapy method of the invention is that expressionof the chimeric pro-caspase need only occur for a short period of time,since, upon oligomerization, apoptosis of the cell occurs. Thus, a genetherapy method of the invention is distinguishable from more typicalgene therapy methods, where prolonged expression of the exogenouslyintroduced gene product is required for a therapeutic effect.

In addition, a method of the invention can supplement current genetherapy procedures. For gene therapy, the exogenous nucleic acidmolecule can be introduced into a patient either in vivo, in which thedesired gene is administered directly to the patient, or ex vivo, inwhich cells are removed from the patient, transfected with desiredgenes, then transplanted back into the patient (see U.S. Pat. No.5,399,346, which is incorporated herein by reference). A challenge ofgene therapy is to develop safe and efficient methods for delivering anexogenous nucleic acid molecule into a cell (see, for example, Andersonet al., supra, 1998; Verma and Somia, supra, 1997; Wilson, supra, 1996).In particular, it can be necessary to ablate a genetically modified cellif the introduction of the exogenous nucleic acid molecule results in anunexpected and undesirable side effect.

Various methods have been utilized to ablate genetically modified cellsfollowing introduction of an exogenous nucleic acid molecule. In onemethod, a gene therapy vector can include an inducible suicide gene,such as the herpes simplex virus thymidine kinase (HSV-TK) gene. Cellscontaining the HSV-TK gene can be killed by treating the cells with thenucleoside analog, ganciclovir, which the HSV-TK gene product convertsto an intermediate that can be incorporated into elongating DNA andresults in death of the cells (Moolten, Cancer Res. 46:5276-5281(1986)). Due to its mechanism of action, however, HSV-TK only killsproliferating cells and, therefore, it is not useful where the targetcells for gene therapy are in a resting state. In addition, the HSV-TKgene is not a human gene and, therefore, the HSV-TK gene product can beimmunogenic to the host.

The death receptor, Fas, also has been used as an agent to kill cells.Aggregation of Fas due to an interaction with its ligand can triggerapoptosis in proliferating and non-proliferating cells (Nagata andGoldstein, Science 267:1449-1456 (1995); Nagata, Cell 88:355-365(1997)). A conditional Fas allele has been made with human FK506 bindingprotein (FKBP), and binds to a number of natural and synthetic ligandswith high affinity. Dimers of these ligands can induce aggregation offusion proteins that contain FKBP. A fusion polypeptide consisting ofFKBP and Fas (FKBP-Fas) allows Fas to be aggregated by dimeric ligands,leading to cell death (Amara et al., supra, 1997; Clackson et al.,supra, 1998; Spencer, supra, 1996). Since the FKBP-Fas consists of humanproteins, it is non-immunogenic to a human host. However, many celltypes are insensitive to Fas-mediated apoptosis and some cells arestimulated to proliferate upon treatment with Fas (Nagata and Goldstein,supra, 1995; Nagata, supra, 1997), thus limiting the usefulness of Fasas a means to ablate genetically modified cells.

The present invention provides chimeric pro-caspases, which canoligomerize in a cell and, therefore, can be used to selectively induceapoptosis in cell. As such, a polynucleotide encoding a chimericpro-caspase can be included in a vector with an exogenous gene to beintroduced into cells of the subject, or can be introduced in a secondvector in combination with the gene therapy vector. Where it isdesirable to ablate the cells containing the introduced gene therapyvector, for example, due to the termination of the treatment or due tothe incorporation of exogenously introduced gene into a region of thegenome such that a deleterious effect is produced, the co-introducedchimeric pro-caspase can be expressed in the cells, thereby activatingcaspase activity in the cells and inducing apoptosis. Such a methodprovides substantial advantages over the HSV-TK and Fas systems in thatcaspase activation leads to effective cell death in proliferating cellsor non-proliferating cells, and in that the components of thepro-caspase constructs are human proteins, which should notsubstantially elicit an immunological response by the host.

The invention will now be described in greater detail by reference tothe following non-limiting examples.

EXAMPLE I Autoproteolytic Activation of Pro-Caspases by Oligomerization

This example demonstrates that oligomerization of pro-caspases inducesproteolytic generation of mature caspase subunits and activation oftheir cell death activity.

Expression Plasmids

FKBP12 and FasEC fusions of caspases were constructed in pRK5. ForFKBP12 fusions, a fragment containing three tandem repeats of FKBP12with an N-terminally fused c-Src myristylation signal and a C-terminallyfused HA tag was amplified by polymerase chain reaction (PCR) from pMF3E(Spencer et al., Science 262:1019-1024 (1993), which is incorporatedherein by reference), digested with EcoRI and BamHI, and cloned intopRK5, yielding pFkp3-HA. DNA fragments containing full-length anddeletion mutants of human pro-caspase-8 with a C-terminal FLAG tag weredigested with BamHI and HindIII and cloned into pFkp3-HA. pFkp3 was madeby deleting the SalI/XhoI fragment of caspase-8(180) inpFkp3-Casp8(180).

Murine FasEC (residues 1-189) fusions were made by three-way ligation.For FasEC-Casp1, a BamHI/NcoI fragment of FasEC was ligated to aNcoI/SalI fragment of murine caspase-1 in pRK5. For FasEC-Casp3 andFasEC-Casp8(182), a BamHI/EcoRI fragment of FasEC was ligated with aEcoRI/SalI fragment of human caspase-3 or human caspase-8 residues182-479 in pRK5. Active site cysteine to serine mutants were made by PCRmutagenesis and assembled as for the corresponding wild-type constructs.Each construct was confirmed by partial DNA sequencing andimmunoblotting or in vitro translation. pRK-crmA (Hsu et al., Cell81:495-504 (1995), which is incorporated herein by reference) andpEBB-mFas (Yang et al., Cell 89:1067-1076 (1997), which is incorporatedherein by reference) were as described.

Cell Death Assay

The cell death assay was performed essentially as previously described(Yang et al., supra, 1997). 1.5×10⁵ HeLa cells/well were transfected bythe calcium phosphate precipitation method. For each transfection, 0.25μg of a β-galactosidase reporter plasmid pCMV-lacZ was included and thetotal amount of DNA was adjusted to 1.25 μg with the vector plasmidpRK5. AP1510 dimerizing agent or monomeric FK506 competitor (AriadPharmaceutical, Inc.; Cambridge Mass. ) was added 6 hr aftertransfection as indicated and cells were stained with X-gal 16 hr aftertransfection. For FasEC fusions, Jo2 antibody (PharMingen; San DiegoCalif.) was added as indicated 10 hr after transfection, and cells werestained with X-gal 18 hr after transfection. The percentage of apoptosiswas determined by counting the number of blue cells with apoptoticmorphology and dividing by the total number of blue cells. Specificapoptosis was calculated as the percentage of apoptosis in eachtransfection minus the percentage of apoptosis in the vector-transfectedcells that was not treated with either AP1510 or Jo2. The vector controlwas included in each experiment and showed less than 5% apoptosis. Datashown are the averages and standard deviations of 2 to 4 independentexperiments. For each experiment, 200 or more blue cells were countedfrom randomly chosen fields.

Pro-Caspase Processing in Transfected Cells

7.5×10⁵ 293T cells plated on 35 mm dishes were transfected with 1 μg ofthe indicated expression plasmids by the calcium phosphate method.Eleven hr after transfection, the medium from parallel transfections wasexchanged for medium containing either vehicle or 1 μM AP1510. At theindicated time points, the transfected cells were washed once with icecold PBS and extracted in 100 μl of IP-lysis buffer (Hsu et al., supra,1995). Protein concentrations in extracts were equalized by the Bradfordassay and analyzed by immunoblot for FLAG with ECL (Amersham; UppsalaSweden; anti-FLAG MAb M2; Kodak; Rochester N.Y.; rabbit polyclonalanti-FLAG (Santa Cruz Biochemical Co.; Santa Cruz Calif.).

Cell-Free Processing of Pro-Caspase-8

In vitro transcription and translation of the indicated constructs with³⁵S-labeled methionine were carried out with the TNT Reticulocyte LysateSystem (Promega; Madison Wis.). The reaction mixture contained 1 μl ofthe in vitro translation product and the indicated drugs dissolved in 3μl of CED3 reaction buffer (Xue et al., Genes Devel. 10:1073-1083(1996), which is incorporated herein by reference). Final drugconcentrations of 100 nM of AP1510 or FK506 and 10 μM ofZ-Asp-Glu-Val-Asp (Z-DEVD; Enzyme System Products; CA) were used. Thereaction mixture was incubated in 30° C. for 4 hr, then the reactionstopped by the addition of SDS sample buffer. Reaction products werevisualized by SDS-PAGE and autoradiography.

Apoptosis Mediated by Pro-Caspase-8 Requires Its DED Domains

Overexpression of full-length pro-caspase-8 potently induces cell death(Boldin et al., supra, 1996; Muzio et al., supra,. 1996). Since DEDdomains can mediate homophilic interactions, the ability of DED domainsto oligomerize pro-caspase-8 molecules and activate them was examined.Wild-type pro-caspase-8 and mutants missing the DED domains were fusedto a protein motif that allowed inducible oligomerization. Each fusionprotein contained three tandem repeats of the FK506 binding protein (seeFIG. 1A; “Fkp”), which is induced to oligomerize by addition of thedivalent small chemical ligand such as AP1510 (Amara et al., supra,1997). To facilitate membrane localization and product detection, fusionproteins carried an N-terminal c-Src myristylation signal and containeda hemagglutinin (HA) tag and a FLAG tag at the fusion junction and the Cterminus, respectively; the C-terminal epitope tag does not interferewith p10 generation or caspase function (Xue et al., supra, 1996).

In the absence of the dimerizing agent (AP1510), expression ofFkp3-Casp8 in HeLa cells potently induced apoptosis (FIG. 1B). Theapoptotic cells showed the characteristic morphologies of membraneblebbing, pyknosis, and rounding up of the cell body. The cell deathactivity of Fkp3-Casp8 was blocked by the poxvirus serpin inhibitor,crmA, consistent with previous results (Boldin et al., supra, 1996;Muzio et al., supra, 1996). In contrast to the full length pro-caspase-8fusion, three mutants that lack the DED domains demonstratedmuch-reduced apoptosis (1B), indicating that the DED domains ofpro-caspase-8 are required for its cell death activity.

Activation of Pro-Caspase-8 by FKBP-Mediated Oligomerization

If the function of DED domains is to oligomerize pro-caspase-8molecules, then oligomerization of the Fkp3-caspase-8 mutants by AP1510should restore their apoptotic activity. Fkp3-Casp8(180) caused littlecell death in the absence of the dimerizing agent (less than 5%; FIG. 1Band FIG. 2A). Addition of AP1510 caused a dose-dependent increase ofapoptosis in HeLa cells expressing Fkp3-Casp8(180). Similar results wereobserved when 293T cells were used for transfection. At an AP1510concentration of 500 nM, more than 40% of transfected cells underwentapoptosis (FIG. 2A), which is comparable to the level observed in cellsexpressing Fkp3-Casp8. Addition of the monomeric, competitive FKBPligand, FK506, inhibited this apoptotic effect. In addition, Fkp3, whichconsists of only the tandem FKBP12 domains (FIG. 1A), caused adominant-negative inhibition of killing induced by AP1510 (FIG. 2A). Thecell killing induced by Fkp3-Casp8(180) also was inhibited by crmA. In acontrol experiment, mutation of the active site cysteine (C360S) inFkp3-Casp8(180) abolished the apoptotic activity in the presence ofdimerizing agent. These results demonstrate that oligomerization of theprotease domain of pro-caspase-8 activates its killing activity and thatcell death induced by oligomerization is dependent on the intrinsiccaspase activity of caspase-8.

As with Fkp3-Casp8(180), the addition of AP1510 also activated theapoptotic activity of Fkp3-Casp8(206) (FIG. 2B). Both constructs containresidue Asp-216, which is recognized during the processing ofpro-caspase-8 (Medema et al., supra, 1997). In contrast, killing byFkp3-Casp8(217), which lacks this cleavage recognition residue, did notincrease with the addition of AP1510 (FIG. 2B). This result indicatesthat pro-caspase processing at residue 216 may be required forgenerating active caspase and, therefore, for oligomerization-inducedkilling.

Fas Extracellular Domain-Mediated Oligomerization of Three Pro-Caspases

To confirm that oligomerization activates pro-caspase-8, an alternativestrategy of inducing oligomerization through a membrane-bound receptor,using the extracellular domain of murine Fas (FasEC, FIG. 3A), wasexamined. The FasEC was used for these studies because of theavailability of its agonistic antibody, Jo2, which is a pentameric IgMantibody that allows effective oligomerization (Ogasawara et al., Nature364:806-809 (1993), which is incorporated herein by reference). SinceJo2 does not recognize human Fas, it has no toxic effect on human celllines. In addition, by making a FasEC fusion of the protease domain ofpro-caspase-8 (FasEC-Casp8(182)), several intermediaries thatparticipate in the in vivo Fas-FADD-pro-caspase-8 connection, includingthe death domain of Fas, FADD, and the DED domains of pro-caspase-8,could be avoided. As such, the function of these protein motifs could beexamined.

Addition of Jo2 did not cause cell death in human HeLa cells expressingFasEC (FIG. 3B). However, addition of Jo2 activated the apoptoticactivity of FasEC-Casp8(182) in a dose-dependent fashion (FIG. 3B). Thelevel of cell death induced by FasEC-Casp8(182) was similar to the levelinduced by wild-type Fas at the maximal Jo2 concentration. Jo2-inducedapoptosis through FasEC-Casp8(182) was blocked by crmA, and a catalyticcysteine-to-serine mutant, FasEC-Casp(182,C360S), did not respond toJo2, again demonstrating that oligomerization-induced death required theintrinsic protease activity of the caspase. These results confirm theresults obtained using the FKBP fusions and indicate that pro-caspase-8can be activated by oligomerization. The results further indicate thatthe intermediary protein motifs between Fas and pro-caspase-8 act tophysically link the pro-caspase-8 protease domain to the ligand-bindingextracellular domain of Fas, thus resulting in activation ofpro-caspase-8.

Pro-caspase-1 and -3 also were examined using the FasEC fusion system inorder to determine whether oligomerization-induced activation is ageneral property of caspases. Pro-caspase-1 contains a long prodomain,similar to pro-caspase-8, but has a different substrate specificity(Thomberry et al., J. Biol. Chem. 272:17907-17911 (1997)). Incomparison, pro-caspase-3 contains a very short prodomain, but itssubstrate specificity overlaps with that of caspase-8 (Thomberry et al.,supra, 1997). Similarly to the results observed for pro-caspase-8, Jo2activated apoptosis by a fusion of FasEC with pro-caspase-1(FasEC-Casp1) in a dose-dependent manner (FIG. 3C). In comparison,FasEC-Casp1(C284S), in which the catalytic cysteine was mutated, causedno death even in the presence of Jo2, demonstrating that intrinsiccaspase-1 protease activity was required for apoptosis to occur.

In contrast to the results obtained using pro-caspase1 andpro-caspase-8, a FasEC fusion of pro-caspase-3, FasEC-Casp3, failed torespond to Jo2 in killing cells, even though FasEC-Casp3 causedsubstantial cell death by itself (FIG. 3C). Similarly to the fusions ofthe other two proteases, FasEC-Casp3(C163S) caused no killing,indicating that killing by FasEC-Casp3 also required its intrinsicprotease activity. Thus, FasEC-Casp3 is not activated byoligomerization, but may be activated by pre-existing cellular caspases.These results indicate that oligomerization-induced activation may be aproperty of initiator caspases, but not of executioner caspases.

Induction of Pro-Caspase Processing by Oligomerization

Oligomerization-induced apoptosis was further characterized by examiningthe fate of pro-caspase proteins in transfected cells with and withoutinduced oligomerization. 293T cells were used in these experimentsbecause of their high transfection efficiency. At DNA concentrationsthat allow detection of transfected gene products by immunoblotting,Fkp3-Casp8(180) induced some apoptosis and was slowly processed in theabsence of dimerizing agent (FIG. 4A, lanes 1-5). The slow processingmay represent the basal probability of membrane-targeted Fkp3-zymogenmolecules randomly encountering one another.

Processing generated two peptides containing the C-terminalFLAG-epitope: p37 (labeled ΔN), which appeared first, and p10. p10likely corresponds to the small subunit in mature caspase-8 (Medema etal., supra, 1997), which is derived from the C terminus ofpro-caspase-8, and p37 is a processing intermediate. In contrast, whenFkp3-Casp8(180) was expressed in the presence of AP1510, the zymogen wascompletely processed after only 1 hour of treatment with dimerizingagent, and only ΔN was completely processed after 2 hours of dimerizingagent treatment (FIG. 4A, lane 7). In the presence of the dimerizingagent, newly synthesized zymogen was rapidly processed and accumulatedas ΔN and p10 FIG. 4A, lanes 8-10). This result indicates thatoligomerization induces the processing of Fkp3-Casp8(180). Moreover,processing required the intrinsic caspase activity of the zymogen. Theactive site C360S mutant of Fkp3-Casp8(180) did not become processed,even in the presence of AP1510 (FIG. 4A, lanes 11-12). Thus,oligomerization does not result in pro-caspases become better substratesfor a pre-existing cellular caspase, but, instead, pro-caspaseprocessing is an autoproteolytic process. These results correspond withthe observation that deletion of one caspase recognition site inFkp3-Casp8(217) blocked processing induced by AP1510 (FIG. 4A, lanes 13and 14), since the caspase retained the ability to oligomerize.

The ability to detect p10 was unexpected because cell death occursquickly upon generation of active caspase-8 in the cytosol. As such, thep10 detected in these experiments likely remains bound to themembrane-targeted Fkp3-zymogen oligomer. In the course of generating themature tetrameric caspase from two zymogen molecules, one zymogen maybeprocessed before the other, producing p20 and p10 subunits that areboundto unprocessed zymogens. As such, p10 is detected indimerizer-treated cells only when there is also some low level of thefull-length zymogen (F4 FIG. 4A, lanes 9 and 10). The cowpox virusserpin inhibitor crmA does not affect pro-caspase-8 processing, butinhibits mature caspase-8 activity (Medema et al., supra, 1997; Muzio etal., supra, 1997). When crmA was coexpressed with Fkp3-Casp8(180),processing was significantly slowed, and the processing intermediate-Nwas observed only in the presence of AP1510 (FIG. 4B).

To circumvent the limitations of intracellular expression experiments, acell-free system was established, in which pro-caspase processing couldbe initiated by inducing oligomerization. The addition of AP1510 to invitro translated, ³⁵S-labeled Fkp3-Casp8(206) led to the proteolyticgeneration of peptides corresponding to the mature caspase-8 subunitsp18 and p10, and three processing intermediates p46, p37, and p20 (FIG.5A). Processing initiated by AP1510 was blocked by the addition ofFK506, the monomeric ligand of FKBP that competes for AP1510 binding,and also was inhibited by the addition of the caspase inhibitor z-DEVD(FIG. 5A). These results demonstrate directly that pro-caspaseprocessing in vitro requires oligomerization and caspase activity.Fkp3-Casp8(217) served as a negative control and was incapable of beingprocessed in the presence of AP1510 (F5 FIG. 5A). In the absence of thein vitro translated pro-caspase, the reaction mixture contained nocaspase activity, as demonstrated by the lack of PARP cleavage in thepresence of AP1510.

Based on time course experiments (FIG. 5B), relative band intensitiesnormalized by the known methionine content of the predicted peptides,comigration with known truncation mutants, and the presence of theC-terminal FLAG epitope tag, the identities of the proteolytic productstentatively could be assigned (FIG. 5B) and a model of pro-caspaseprocessing identified. First, the prodomain was separated from theprotease domain, generating p46 and p37. p46 corresponded to theN-terminal Fkp3, and p37 corresponded to ΔN (see FIG. 4) and consistedof the protease domain. Second, the protease domain was cleaved togenerate p20 and p10. p20 then was processed to p18. p18 and p10 are themature subunits of caspase-8 that can associate to form a tetramericenzyme. Consistent with this sequence of cleavages, deletion of thepredicted first cleavage site in Fkp3-Casp8(217) completely blockedprocessing (F4 FIG. 4A, FIG. 5A). Taking FKBP-fused pro-caspase-8 as amodel, these results collectively demonstrate that oligomerizationinduces autoproteolytic processing of pro-caspases in vivo and in vitro.

EXAMPLE II Preparation and Characterization of Chimeric Pro-Caspase

This example describes the construction and characterization of viralvectors expressing an FKBP-pro-caspase fusion polypeptide that caneffectively induce apoptosis upon oligomerization, but that otherwisedemonstrates minimal autotoxicity.

For oligomerization of caspases to be an effective suicide system, thecaspase should have maximal cytotoxicity in the presence of a dimerizingagent, but minimal cytotoxicity in the absence of the dimerizer. Thehuman FKBP protein is used for the oligomerization motif. The efficacyof FKBP dimerization has been demonstrated in various cells for diversebiological processes (Spencer et al., supra, 1993; Amara et al., supra,1997; Freiberg et al., J. Invest. Dermatol. 108:215-219 (1997); Freiberget al., J. Biol. Chem. 271:31666-31669 (1996); Holsinger et al., Proc.Natl. Acad. Sci., USA 92:9810-9814 (1995)). To minimize the binding ofdimeric ligands to endogenous FKBP, the FKBP-ligand interface wasredesigned to generate a ligand, AP1903, which is specific to a FKBPderivative Fv (Clackson et al., supra, 1998)). AP1903 and Fv areavailable from Ariad pharmaceutical, Inc. Two copies of Fv are fused tothe pro-caspase (see FIG. 6) to facilitate oligomerization; using morecopies of Fv was not necessary (Clackson et al., supra, 1998).

Numerous caspases have been cloned, and the selection of a caspase foruse in a cell suicide system is based, on several factors. For example,the caspase should have substrate specificity similar to the executionercaspase to ensure cleavage of cellular substrates. In addition, thepresence of a pro-domain, which sometime mediates homotypic interactionamong pro-caspase molecules, can be useful because it can enhance theoligomerization. At high expression level, however, the presence ofprodomain may result in autotoxicity. Caspase-8 is particularly usefulbecause it has substrate specificity similar to caspase-3, which cleavesmost cell death substrates identified so far. Caspase-8 contains withinits pro-domain two DED domains, which can interact homotypically. The C.elegans caspase CED-3 is another useful caspase because, similarly tocaspase-8, it effectively cleaves cellular substrates and its pro-domaincan self-associate. The nucleic acid construct is cloned into aretroviral expression vector or other viral vector commonly used forlong term expression of transgene.

Full length or various mutants of pro-caspase-8 or any other selectedcaspase is fused to two copies of Fv in the murine stem cell virus(MSCV) retroviral vector, MIG R1 (FIG. 6; Pear et al., Blood 92:3780-3792 (1998), which is incorporated herein by reference). The retroviralLTR of MSCV provides high level protein expression in various cells,including embryonic carcinoma and embryonic stem cells, and the presenceof extended retroviral package sites in MIG R1 allows maximal retroviralproduction. A humanized green fluorescent protein expressed from aninternal ribosomal entry sites allows visualization and fluorescenceactivated cell sorting (FACS) analysis of transduced cells (see FIG. 6).

For viral production, vectors expressing Fv-caspase-8 fusionpolypeptides (Fv-casp8) are transfected into BOSC cells, which is apackaging cell line derived from the highly transfectable 293 cell line.BOSC cells can produce high titer, helper virus-free retroviruses within48 hr (Pear et al., Proc. Natl. Acad. Sci., USA 90:8392-8396 (1993),which is incorporated herein by reference). The Fv-casp8 expressingviruses produced in the BOSC cells are harvested and used to infect 3T3cells.

Autotoxicity of Fv-casp8 viruses is evaluated by comparing thepercentage of apoptotic cells in Fv-casp8 virus-infected 3T3 cells withthe percentage in MIG R1-infected 3T3 cells. Percentage of apoptoticcells are counted as described by Yang et al. (supra, 1997). Apoptoticcells are identified by cell body shrinkage, membrane blebbing, anddetachment from plates. Transfected cells are identified by detectingthe expression of GFP. Fv-casp8-expressing viruses that, withoutinduction, cause only a low-level of cell death are selected.AP1903-induced apoptosis in Fv-casp8 transfected cells is assayed byculturing Fv-casp8-infected 3T3 cells in the presence of variousconcentration of AP1903. Percentage of apoptotic cells are counted andthe Fv-casp8 expressing vectors that demonstrate high sensitivity toAP1903 are selected.

These experiments allow the selection of optimal Fv-casp8 constructsthat demonstrate minimal autotoxicity in the absence of AP1903, butachieve maximal apoptosis when induced to oligomerize in the presence ofAP1903. Furthermore, since caspases often act in a cascade, two genescan be introduced into a cell to be treated, including a gene encodingan Fv-caspase fusion, which serves as a initiator caspase, and a genethat acts as an executioner caspase to amplify the cell death signal.

The selected Fv-caspase vectors are examined using an in vivo modelsystem. Viral vectors expressing the optimal Fv-casp8 fusion are used toinfect mouse bone marrow cells, then the transfected cells are used toreconstitute lethally irradiated recipient mice. The use of areconstitution assay allows an assessment of whether 1) the Fv-casp8transgene interferes with development and differentiation of infectedstem cells, and 2) AP1903 can kill, in vivo and in vitro, variouslineage cells derived from the infected bone marrow cells. A murinechronic myelogenous leukemia model has been established using a similarprocedure (Pear et al., Blood 92:3780-3792 (1998), which is incorporatedherein by reference). The efficacy of the optimal Fv-casp8 vector thenwill be examined by infecting tumor cells with the Fv-casp8 expressingviruses, transplanting the infected tumor cells into mice, administeringAP1903 to the mice, and monitoring tumor formation.

For bone marrow transplantation, donor mice are primed with5-fluorouracil. Bone marrow cells are isolated and pre-incubated withinterleukin-3 (IL-3), IL-6, and stem cell factor (SCF). The bone marrowcells then are co-cultivated with BOSC cells that have been transfectedwith Fv-casp8 vector. Infected marrow cells are selected by FACS sortingfor GFP expression, and transplanted into lethally irradiatedrecipients. Hematopoiesis in the recipient is followed closely.Expression of Fv-casp8 protein in hematopoietic tissues is examined byimmunoblotting with anti-Flag monoclonal antibody. The myeloid andlymphoid lineages in the reconstituted recipient are examined for theirfunctions and their sensitivity to AP1903. Cell death is examined bypropidium iodide staining, followed by FACS analysis.

For tumor formation, MOPC-11 murine myeloma cells are infected with theFv-casp8 viruses. Infected cells are isolated by FACS sorting andimplanted in Balb/c mice. AP1903 is injected into the animals and tumordevelopment is monitored. These experiements can demonstrate whether theFv-casp8 transgene interferes with the functions of the infected cellsand whether the infected cells are killed effectively in vitro and invivo by AP1903.

While the invention has been described in detail with reference to theexamples provided above, it will be understood that modifications andvariations are within the spirit and scope of that which is describedand claimed. Accordingly, the invention is limited only by the followingclaims.

1. A chimeric pro-caspase, comprising a pro-caspase domain and anoligomerizing domain.
 2. The chimeric pro-caspase of claim 1, whereinthe pro-caspase domain comprises pro-caspase-8 or a peptide portion ofsaid pro-caspase-8 having caspase-8 activity potential.
 3. The chimericpro-caspase of claim 1, wherein the pro-caspase domain comprises apro-caspase form of an initiator caspase or a peptide portion of saidpro-caspase having initiator caspase activity potential.
 4. The chimericpro-caspase of claim 1, wherein the oligomerizing domain comprises anFK506 binding protein.
 5. The chimeric pro-caspase of claim 1, whereinthe oligomerizing domain comprises a polypeptide that interactsspecifically with cellular protein in the cell.
 6. The chimericpro-caspase of claim 5, wherein the oligomerizing domain comprises a Rafdomain, which interacts specifically with a Ras cellular protein.
 7. Thechimeric pro-caspase of claim 5, wherein the oligomerizing domaincomprises a guanine exchange factor domain, which interacts specificallywith a Ras cellular protein.
 8. The chimeric pro-caspase of claim 1,further comprising a protein transduction domain.
 9. The chimericpro-caspase of claim 8, wherein the protein transduction domain is thehuman immunodeficiency virus TAT protein transduction domain.
 10. Thechimeric pro-caspase of claim 1, further comprising a cell compartmentlocalization domain.
 11. A pharmaceutical composition, comprising achimeric pro-caspase of claim
 1. 12. An antibody that reactsspecifically with a chimeric pro-caspase of claim
 1. 13. A kitcomprising an antibody of claim
 12. 14. A polynucleotide encoding achimeric pro-caspase of claim
 1. 15. The polynucleotide of claim 14,which is contained in a vector.
 16. The polynucleotide of claim 15,wherein the vector is an expression vector.
 17. The polynucleotide ofclaim 16, wherein the expression vector is a viral vector.
 18. A hostcell containing the vector of claim
 15. 19. An oligonucleotide, whichhybridizes specifically with a polynucleotide of claim
 14. 20. Apharmaceutical composition comprising the polynucleotide of claim 14.21. A method of inducing apoptosis in a cell, comprising providing achimeric pro-caspase in the cell, wherein the chimeric pro-caspasecomprises a pro-caspase domain and an oligomerizing domain, and wherebythe chimeric pro-caspase forms an oligomer in the cell, therebyactivating caspase activity of the chimeric pro-caspase and inducingapoptosis in the cell.
 22. The method of claim 21, wherein providing thechimeric pro-caspase comprises introducing a polynucleotide encoding thechimeric pro-caspase into the cell, and expressing the encoded chimericpro-caspase.
 23. The method of claim 22, wherein the polynucleotideencoding the chimeric pro-caspase is contained in a vector.
 24. Themethod of claim 23, wherein the vector is a viral vector.
 25. The methodof claim 21, wherein the chimeric pro-caspase further comprises aprotein transduction domain, and wherein providing the chimericpro-caspase comprises contacting the cell with the chimeric pro-caspasecomprising the protein transduction domain.
 26. The method of claim 25,wherein the protein transduction domain is the human immunodeficiencyvirus TAT protein transduction domain.
 27. The method of claim 21,wherein the pro-caspase domain comprises a pro-caspase form of aninitiator caspase or a peptide portion of said pro-caspase havinginitiator caspase activity potential.
 28. The method of claim 21,wherein the pro-caspase domain comprises pro-caspase-8 or a peptideportion of said pro-caspase-8 having caspase-8 activity potential. 29.The method of claim 21, wherein the chimeric pro-caspase is induced toform an oligomer in the cell.
 30. The method of claim 29, wherein theoligomerizing domain of the chimeric pro-caspase comprises an FK506binding protein, and wherein the chimeric pro-caspase is induced to forman oligomer due to contacting the cell with an agent that inducesoligomerization of FK506 binding proteins. 31-45. (canceled)